chore(release): v0.5.3

Co-authored-by: Roman Nurik <roman@nurik.net>

.gemini/commands/find-docs.toml

@@ -0,0 +1,30 @@
+description = "Find relevant documentation and output GitHub URLs."
+
+prompt = """
+## Mission: Find Relevant Documentation
+
+Your task is to find documentation files relevant to the user's question within the current git repository and provide a list of GitHub URLs to view them.
+
+### Workflow:
+
+1.  **Identify Repository Details**:
+    *   You may use shell commands like `git` or `gh` to get the remote URL of the repository.
+    *   From the remote URL, parse and construct the base GitHub URL (e.g., `https://github.com/user/repo`). You must handle both HTTPS (`https://github.com/user/repo.git`) and SSH (`git@github.com:user/repo.git`) formats.
+    *   Determine the default branch name. You can assume `main` for this purpose, as it is the most common.
+
+2.  **Search for Documentation**:
+    *   First, perform a targeted search across the repository for documentation files (e.g., `.md`, `.mdx`) that seem directly related to the user's question.
+    *   If this initial search yields no relevant results, and a `docs/` directory exists, read the content of all files within the `docs/` directory to find relevant information.
+    *   If you still can't find a direct match, broaden your search to include related concepts and synonyms of the keywords in the user's question.
+    *   For each file you identify as potentially relevant, read its content to confirm it addresses the user's query.
+
+3.  **Construct and Output URLs**:
+    *   For each file you identify as relevant, construct the full GitHub URL by combining the base URL, branch, and file path. **Do not use shell commands for this step.**
+    *   The URL format should be: `{BASE_GITHUB_URL}/blob/{BRANCH_NAME}/{PATH_TO_FILE_FROM_REPO_ROOT}`.
+    *   Present the final list to the user as a markdown list. Each item in the list should be the URL to the document, followed by a short summary of its content.
+    *   If, after all search attempts, you cannot find any relevant documentation, ask the user clarifying questions to better understand their needs. Do not return any URLs in this case.
+
+### QUESTION:
+
+{{args}}
+"""

.gemini/commands/github/cleanup-back-to-main.toml

@@ -0,0 +1,13 @@
+description = "Go back to main and clean up the branch."
+
+prompt = """
+I'm done with the work on this branch, and I'm ready to go back to main and clean up.
+
+Here is the workflow I'd like you to follow:
+
+1.  **Get Current Branch:** First, I need you to get the name of the current branch and save it.
+2.  **Branch Check:** Check if the current branch is `main`. If it is, I need you to stop and let me know.
+3.  **Go to Main:** Next, I need you to checkout the main branch.
+4.  **Pull Latest:** Once you are on the main branch, I need you to pull down the latest changes to make sure I'm up to date.
+5.  **Branch Cleanup:** Finally, I need you to delete the branch that you noted in the first step.
+"""

.gemini/commands/oncall/pr-review.toml

@@ -0,0 +1,47 @@
+description = "Review a specific pull request"
+
+prompt = """
+## Mission: Comprehensive Pull Request Review
+
+Today, our mission is to meticulously review community pull requests (PRs) for this project. We will proceed systematically, evaluating each candidate PR for its quality, adherence to standards, and readiness for merging.
+
+### Workflow:
+
+1.  **PR Preparation & Initial Assessment**:
+    * **You will check out the designated PR {{args}}** into a temporary branch.
+    * **Execute the preflight checks (`npm run preflight`)**. This includes building, linting, and running all unit tests.
+    * Analyze the output of these preflight checks, noting any failures, warnings, or linting issues.
+
+2.  **In-Depth Code Review**:
+    * **Your primary role is to conduct a thorough and in-depth code review** of the changes introduced in the PR. Focus your analysis on the following criteria:
+        * **Correctness**: Does the code achieve its stated purpose without bugs or logical errors?
+        * **Maintainability**: Is the code clean, well-structured, and easy to understand and modify in the future? Consider factors like code clarity, modularity, and adherence to established design patterns.
+        * **Readability**: Is the code well-commented (where necessary) and consistently formatted according to our project's coding style guidelines?
+        * **Efficiency**: Are there any obvious performance bottlenecks or resource inefficiencies introduced by the changes?
+        * **Security**: Are there any potential security vulnerabilities or insecure coding practices?
+        * **Edge Cases and Error Handling**: Does the code appropriately handle edge cases and potential errors?
+        * **Testability**: Is the new or modified code adequately covered by tests (even if preflight checks pass)? Suggest additional test cases that would improve coverage or robustness.
+    * Based on your analysis, you will determine if the PR is **safe to merge**.
+
+3.  **Reviewing Previous Feedback**:
+    * **Access and examine the PR's history** to identify any **outstanding requests or unresolved comments from previous reviews**. Incorporate these into your current review and explicitly highlight if they have been adequately addressed in the current state of the PR.
+
+4.  **Decision and Output Generation**:
+    * **If the PR is deemed safe to merge** (after your comprehensive review and considering previous feedback):
+        * Draft a **friendly, concise, and professional approval message**.
+        * **The approval message should:**
+            * Clearly state that the PR is approved.
+            * Briefly acknowledge the quality or value of the contribution (e.g., "Great work on X feature!" or "Appreciate the fix for Y issue!").
+            * **Do NOT mention the preflight checks or unit testing**, as these are internal processes.
+            * Be suitable for public display on GitHub.
+    * **If the PR is NOT safe to merge**:
+        * Provide a **clear, constructive, and detailed summary of the issues found**.
+        * Suggest **specific actionable changes** required for the PR to become merge-ready.
+        * Ensure the feedback is professional and encourages the contributor.
+
+### Post-PR Action:
+
+* After providing your review and decision for the current PR, I will wait for you to perform any manual testing you wish to do. Please let me know when you are finished.
+* Once you have confirmed that you are done, I will switch to the `main` branch, clean up the local branch, and perform a pull to ensure we are synchronized with the latest upstream changes for the next review.
+
+"""

.github/workflows/ci.yml

@@ -94,6 +94,10 @@ jobs:
           node-version-file: '.nvmrc'
           cache: 'npm'
 
+      - name: 'Run lockfile check'
+        run: |-
+          npm run check:lockfile
+
       - name: 'Install dependencies'
         run: |-
           npm ci
@@ -367,3 +371,27 @@ jobs:
 
       - name: 'Perform CodeQL Analysis'
         uses: 'github/codeql-action/analyze@df559355d593797519d70b90fc8edd5db049e7a2' # ratchet:github/codeql-action/analyze@v3
+
+  # Check for changes in bundle size.
+  bundle_size:
+    name: 'Check Bundle Size'
+    if: |-
+      ${{ github.event_name != 'merge_group' }}
+    runs-on: 'ubuntu-latest'
+    permissions:
+      contents: 'read' # For checkout
+      pull-requests: 'write' # For commenting
+
+    steps:
+      - name: 'Checkout'
+        uses: 'actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8' # ratchet:actions/checkout@v5
+        with:
+          fetch-depth: 1
+
+      - uses: 'preactjs/compressed-size-action@946a292cd35bd1088e0d7eb92b69d1a8d5b5d76a'
+        with:
+          repo-token: '${{ secrets.GITHUB_TOKEN }}'
+          pattern: './bundle/**/*.{js,sb}'
+          minimum-change-threshold: '1000'
+          compression: 'none'
+          clean-script: 'clean'

.github/workflows/e2e.yml

@@ -4,30 +4,62 @@ on:
   push:
     branches:
       - 'main'
+  # This will run for PRs from the base repository, providing secrets.
+  pull_request:
+    branches:
+      - 'main'
+      - 'release/**'
+  # This will run for PRs from forks when a label is added.
+  pull_request_target:
+    types: ['labeled']
   merge_group:
 
 jobs:
-  e2e-test-linux:
-    name: 'E2E Test (Linux) - ${{ matrix.sandbox }}'
-    runs-on: 'ubuntu-latest'
+  e2e-test:
+    name: 'E2E Test (${{ matrix.os }}) - ${{ matrix.sandbox }}'
+    # This condition ensures the job runs for pushes to main, merge groups,
+    # PRs from the base repo, OR PRs from forks with the correct label.
+    if: |
+      github.event_name == 'push' ||
+      github.event_name == 'merge_group' ||
+      (github.event.pull_request.head.repo.full_name == github.repository) ||
+      (github.event.label.name == 'maintainer:e2e:ok')
+    runs-on: '${{ matrix.os }}'
     strategy:
+      fail-fast: false
       matrix:
+        os:
+          - 'ubuntu-latest'
+          - 'macos-latest'
+          - 'gemini-cli-windows-16-core'
         sandbox:
           - 'sandbox:none'
           - 'sandbox:docker'
         node-version:
           - '20.x'
-          - '22.x'
-          - '24.x'
+        exclude:
+          # Docker tests are not supported on macOS or Windows
+          - os: 'macos-latest'
+            sandbox: 'sandbox:docker'
+          - os: 'gemini-cli-windows-16-core'
+            sandbox: 'sandbox:docker'
+
     steps:
-      - name: 'Checkout'
+      - name: 'Checkout (fork)'
         uses: 'actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8' # ratchet:actions/checkout@v5
+        if: "github.event_name == 'pull_request_target'"
+        with:
+          ref: '${{ github.event.pull_request.head.sha }}'
+          repository: '${{ github.event.pull_request.head.repo.full_name }}'
+
+      - name: 'Checkout (internal)'
+        uses: 'actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8' # ratchet:actions/checkout@v5
+        if: "github.event_name != 'pull_request_target'"
 
       - name: 'Set up Node.js ${{ matrix.node-version }}'
-        uses: 'actions/setup-node@49933ea5288caeca8642d1e84afbd3f7d6820020' # ratchet:actions/setup-node@v4
+        uses: 'actions/setup-node@49933ea5288caeca8642d1e84afbd3f7d6820020' # ratchet:actions-node@v4
         with:
           node-version: '${{ matrix.node-version }}'
-          cache: 'npm'
 
       - name: 'Install dependencies'
         run: |-
@@ -39,50 +71,15 @@ jobs:
 
       - name: 'Set up Docker'
         if: |-
-          ${{ matrix.sandbox == 'sandbox:docker' }}
+          matrix.os == 'ubuntu-latest' && matrix.sandbox == 'sandbox:docker'
         uses: 'docker/setup-buildx-action@e468171a9de216ec08956ac3ada2f0791b6bd435' # ratchet:docker/setup-buildx-action@v3
 
-      - name: 'Set up Podman'
-        if: |-
-          ${{ matrix.sandbox == 'sandbox:podman' }}
-        uses: 'redhat-actions/podman-login@4934294ad0449894bcd1e9f191899d7292469603' # ratchet:redhat-actions/podman-login@v1
-        with:
-          registry: 'docker.io'
-          username: '${{ secrets.DOCKERHUB_USERNAME }}'
-          password: '${{ secrets.DOCKERHUB_TOKEN }}'
-
       - name: 'Run E2E tests'
         env:
           GEMINI_API_KEY: '${{ secrets.GEMINI_API_KEY }}'
           KEEP_OUTPUT: 'true'
           SANDBOX: '${{ matrix.sandbox }}'
           VERBOSE: 'true'
+        shell: 'bash'
         run: |-
           npm run "test:integration:${SANDBOX}"
-
-  e2e-test-macos:
-    name: 'E2E Test - macOS'
-    runs-on: 'macos-latest'
-    steps:
-      - name: 'Checkout'
-        uses: 'actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8' # ratchet:actions/checkout@v5
-
-      - name: 'Set up Node.js'
-        uses: 'actions/setup-node@49933ea5288caeca8642d1e84afbd3f7d6820020' # ratchet:actions/setup-node@v4
-        with:
-          node-version-file: '.nvmrc'
-          cache: 'npm'
-
-      - name: 'Install dependencies'
-        run: |-
-          npm ci
-
-      - name: 'Build project'
-        run: |-
-          npm run build
-
-      - name: 'Run E2E tests'
-        env:
-          GEMINI_API_KEY: '${{ secrets.GEMINI_API_KEY }}'
-        run: |-
-          npm run test:e2e

.github/workflows/gemini-automated-issue-triage.yml

@@ -16,7 +16,7 @@ on:
         type: 'number'
 
 concurrency:
-  group: '${{ github.workflow }}-${{ github.event.issue.number }}'
+  group: '${{ github.workflow }}-${{ github.event.issue.number || github.event.inputs.issue_number }}'
   cancel-in-progress: true
 
 defaults:
@@ -29,22 +29,51 @@ permissions:
   issues: 'write'
   statuses: 'write'
   packages: 'read'
+  actions: 'write' # Required for cancelling a workflow run
 
 jobs:
   triage-issue:
     if: |-
       github.repository == 'google-gemini/gemini-cli' &&
-      (github.event_name == 'issues' ||
-       github.event_name == 'workflow_dispatch' ||
-       (github.event_name == 'issue_comment' &&
-       contains(github.event.comment.body, '@gemini-cli /triage') &&
-       (github.event.comment.author_association == 'OWNER' ||
-        github.event.comment.author_association == 'MEMBER' ||
-        github.event.comment.author_association == 'COLLABORATOR')))
+      (
+        github.event_name == 'workflow_dispatch' ||
+        (
+          (github.event_name == 'issues' || github.event_name == 'issue_comment') &&
+          contains(github.event.issue.labels.*.name, 'status/need-triage') &&
+          (github.event_name != 'issue_comment' || (
+            contains(github.event.comment.body, '@gemini-cli /triage') &&
+            (github.event.comment.author_association == 'OWNER' || github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'COLLABORATOR')
+          ))
+        )
+      )
     timeout-minutes: 5
     runs-on: 'ubuntu-latest'
-
     steps:
+      - name: 'Get issue data for manual trigger'
+        id: 'get_issue_data'
+        if: |-
+          github.event_name == 'workflow_dispatch'
+        uses: 'actions/github-script@60a0d83039c74a4aee543508d2ffcb1c3799cdea'
+        with:
+          github-token: '${{ secrets.GITHUB_TOKEN }}'
+          script: |
+            const { data: issue } = await github.rest.issues.get({
+              owner: context.repo.owner,
+              repo: context.repo.repo,
+              issue_number: ${{ github.event.inputs.issue_number }},
+            });
+            core.setOutput('title', issue.title);
+            core.setOutput('body', issue.body);
+            core.setOutput('labels', issue.labels.map(label => label.name).join(','));
+            return issue;
+
+      - name: 'Check for triage label on manual trigger'
+        if: |-
+          github.event_name == 'workflow_dispatch' && !contains(steps.get_issue_data.outputs.labels, 'status/need-triage')
+        run: |
+          echo "Issue #${{ github.event.inputs.issue_number }} does not have the 'status/need-triage' label. Stopping workflow."
+          exit 1
+
       - name: 'Checkout'
         uses: 'actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8' # ratchet:actions/checkout@v5
 
@@ -60,7 +89,7 @@ jobs:
         id: 'get_labels'
         uses: 'actions/github-script@60a0d83039c74a4aee543508d2ffcb1c3799cdea'
         with:
-          github-token: '${{ steps.generate_token.outputs.token || secrets.GITHUB_TOKEN }}'
+          github-token: '${{ steps.generate_token.outputs.token }}'
           script: |-
             const { data: labels } = await github.rest.issues.listLabelsForRepo({
               owner: context.repo.owner,
@@ -76,9 +105,12 @@ jobs:
         id: 'gemini_issue_analysis'
         env:
           GITHUB_TOKEN: '' # Do not pass any auth token here since this runs on untrusted inputs
-          ISSUE_TITLE: '${{ github.event.issue.title }}'
-          ISSUE_BODY: '${{ github.event.issue.body }}'
-          ISSUE_NUMBER: '${{ github.event.issue.number }}'
+          ISSUE_TITLE: >-
+            ${{ github.event_name == 'workflow_dispatch' && steps.get_issue_data.outputs.title || github.event.issue.title }}
+          ISSUE_BODY: >-
+            ${{ github.event_name == 'workflow_dispatch' && steps.get_issue_data.outputs.body || github.event.issue.body }}
+          ISSUE_NUMBER: >-
+            ${{ github.event_name == 'workflow_dispatch' && github.event.inputs.issue_number || github.event.issue.number }}
           REPOSITORY: '${{ github.repository }}'
           AVAILABLE_LABELS: '${{ steps.get_labels.outputs.available_labels }}'
         with:
@@ -104,18 +136,20 @@ jobs:
             ## Role
 
             You are an issue triage assistant. Analyze the current GitHub issue
-            and identify the most appropriate existing labels. Use the available
+            and identify the most appropriate existing labels by only using the provided data. Use the available
             tools to gather information; do not ask for information to be
-            provided. Do not remove labels titled help wanted or good first issue.
+            provided. Do not remove the following labels titled maintainer,  help wanted or good first issue.
 
             ## Steps
 
-            1. Review the available labels in the environment variable: "${AVAILABLE_LABELS}".
+            1. You are only able to use the echo command. Review the available labels in the environment variable: "${AVAILABLE_LABELS}".
             2. Review the issue title and body provided in the environment variables: "${ISSUE_TITLE}" and "${ISSUE_BODY}".
-            3. Ignore any existing priorities or tags on the issue. Just report your findings.
-            4. Select the most relevant labels from the existing labels, focusing on kind/*, area/*, sub-area/* and priority/*. For area/* and kind/* limit yourself to only the single most applicable label in each case.
+            3. Select the most relevant labels from the existing labels, focusing on kind/*, area/*, sub-area/* and priority/*. For area/* and kind/* limit yourself to only the single most applicable label in each case.
+            4. If the issue already has area/ label, dont try to change it. Similarly, if the issue already has a kind/ label don't change it. And if the issue already has a priority/ label do not change it for example:
+               If an issue has area/core and kind/bug  you will only add a priority/ label.
+               Instead if an issue has no labels, you will could add one lable of each kind.
             5. For each issue please check if CLI version is present, this is usually in the output of the /about command and will look like 0.1.5 for anything more than 6 versions older than the most recent should add the status/need-retesting label.
-            6. If you see that the issue doesn't look like it has sufficient information recommend the status/need-information label.
+            6. If you see that the issue doesn't look like it has sufficient information recommend the status/need-information label and leave a comment politely requesting the relevant information, eg.. if repro steps are missing request for repro steps. if version information is missing request for version information into the explanation section below.
             7. Output the appropriate labels for this issue in JSON format with explanation, for example:
                ```
                {"labels_to_set": ["kind/bug", "priority/p0"], "explanation": "This is a critical bug report affecting main functionality"}
@@ -125,6 +159,8 @@ jobs:
                {"labels_to_set": [], "explanation": "Unable to classify this issue with available labels"}
                ```
             9. Use Area definitions mentioned below to help you narrow down issues.
+            10. If you think an issue might be a Priority/P0 do not apply the priority/p0 label. Instead apply a status/manual-triage label and include a note in your explanation.
+            11. If you are uncertain and have not been able to apply one each of kind/, area/ and priority/ , apply the status/manual-triage label.
 
             ## Guidelines
 
@@ -141,7 +177,10 @@ jobs:
 
             Categorization Guidelines:
             P0: Critical / Blocker
-            - A P0 bug is a catastrophic failure that demands immediate attention. It represents a complete showstopper for a significant portion of users or for the development process itself.
+            - A P0 bug is a catastrophic failure that demands immediate attention.
+            - To be a P0 it means almost all users are running into this issue and it is blocking users from being able to use the product.
+            - You would see this in the form of many comments from different developers on the bug.
+            - It represents a complete showstopper for a significant portion of users or for the development process itself.
             Impact:
             - Blocks development or testing for the entire team.
             - Major security vulnerability that could compromise user data or system integrity.
@@ -150,14 +189,17 @@ jobs:
             Qualifier: Is the main function of the software broken?
             Example: The gemini auth login command fails with an unrecoverable error, preventing any user from authenticating and using the rest of the CLI.
             P1: High
-            - A P1 bug is a serious issue that significantly degrades the user experience or impacts a core feature. While not a complete blocker, it's a major problem that needs a fast resolution. Feature requests are almost never P1.
+            - A P1 bug is a serious issue that significantly degrades the user experience or impacts a core feature.
+            - While not a complete blocker, it's a major problem that needs a fast resolution. Feature requests are almost never P1.
+            - Once again this would be affecting many users.
+            - You would see this in the form of comments from different developers on the bug.
             Impact:
             - A core feature is broken or behaving incorrectly for a large number of users or large number of use cases.
             - Review the bug details and comments to try figure out if this issue affects a large set of use cases or if it's a narrow set of use cases.
             - Severe performance degradation making the application frustratingly slow.
             - No straightforward workaround exists, or the workaround is difficult and non-obvious.
             Qualifier: Is a key feature unusable or giving very wrong results?
-            Example: The gemini -p "..." command consistently returns a malformed JSON response or an empty result, making the CLI's primary generation feature unreliable.
+            Example: Gemini CLI enters a loop when making read-many-files tool call. I am unable to break out of the loop and gemini doesn't follow instructions subsequently.
             P2: Medium
             - A P2 bug is a moderately impactful issue. It's a noticeable problem but doesn't prevent the use of the software's main functionality.
             Impact:
@@ -221,19 +263,23 @@ jobs:
           ${{ steps.gemini_issue_analysis.outputs.summary != '' }}
         env:
           REPOSITORY: '${{ github.repository }}'
-          ISSUE_NUMBER: '${{ github.event.issue.number }}'
+          ISSUE_NUMBER: '${{ github.event.issue.number || github.event.inputs.issue_number }}'
           LABELS_OUTPUT: '${{ steps.gemini_issue_analysis.outputs.summary }}'
         uses: 'actions/github-script@60a0d83039c74a4aee543508d2ffcb1c3799cdea'
         with:
-          github-token: '${{ steps.generate_token.outputs.token || secrets.GITHUB_TOKEN }}'
+          github-token: '${{ steps.generate_token.outputs.token }}'
           script: |-
             // Strip code block markers if present
             const rawLabels = process.env.LABELS_OUTPUT;
             core.info(`Raw labels JSON: ${rawLabels}`);
             let parsedLabels;
             try {
-              const trimmedLabels = rawLabels.replace(/^```(?:json)?\s*/, '').replace(/\s*```$/, '').trim();
-              parsedLabels = JSON.parse(trimmedLabels);
+              const jsonMatch = rawLabels.match(/```json\s*([\s\S]*?)\s*```/);
+              if (!jsonMatch || !jsonMatch[1]) {
+                throw new Error("Could not find a ```json ... ``` block in the output.");
+              }
+              const jsonString = jsonMatch[1].trim();
+              parsedLabels = JSON.parse(jsonString);
               core.info(`Parsed labels JSON: ${JSON.stringify(parsedLabels)}`);
             } catch (err) {
               core.setFailed(`Failed to parse labels JSON from Gemini output: ${err.message}\nRaw output: ${rawLabels}`);
@@ -241,32 +287,44 @@ jobs:
             }
 
             const issueNumber = parseInt(process.env.ISSUE_NUMBER);
+            const explanation = parsedLabels.explanation || '';
+            const labelsToSet = parsedLabels.labels_to_set || [];
+            labelsToSet.push('status/bot-triaged');
 
             // Set labels based on triage result
-            if (parsedLabels.labels_to_set && parsedLabels.labels_to_set.length > 0) {
+            if (labelsToSet.length > 0) {
               await github.rest.issues.setLabels({
                 owner: context.repo.owner,
                 repo: context.repo.repo,
                 issue_number: issueNumber,
-                labels: parsedLabels.labels_to_set
+                labels: labelsToSet
               });
-              const explanation = parsedLabels.explanation ? ` - ${parsedLabels.explanation}` : '';
-              core.info(`Successfully set labels for #${issueNumber}: ${parsedLabels.labels_to_set.join(', ')}${explanation}`);
+              const explanationInfo = explanation ? ` - ${explanation}` : '';
+              core.info(`Successfully set labels for #${issueNumber}: ${labelsToSet.join(', ')}${explanationInfo}`);
             } else {
               // If no labels to set, leave the issue as is
-              const explanation = parsedLabels.explanation ? ` - ${parsedLabels.explanation}` : '';
-              core.info(`No labels to set for #${issueNumber}, leaving as is${explanation}`);
+              const explanationInfo = explanation ? ` - ${explanation}` : '';
+              core.info(`No labels to set for #${issueNumber}, leaving as is${explanationInfo}`);
+            }
+
+            if (explanation) {
+              await github.rest.issues.createComment({
+                owner: context.repo.owner,
+                repo: context.repo.repo,
+                issue_number: issueNumber,
+                body: explanation,
+              });
             }
 
       - name: 'Post Issue Analysis Failure Comment'
         if: |-
           ${{ failure() && steps.gemini_issue_analysis.outcome == 'failure' }}
         env:
-          ISSUE_NUMBER: '${{ github.event.issue.number }}'
+          ISSUE_NUMBER: '${{ github.event.issue.number || github.event.inputs.issue_number }}'
           RUN_URL: '${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}'
         uses: 'actions/github-script@60a0d83039c74a4aee543508d2ffcb1c3799cdea'
         with:
-          github-token: '${{ steps.generate_token.outputs.token || secrets.GITHUB_TOKEN }}'
+          github-token: '${{ steps.generate_token.outputs.token }}'
           script: |-
             github.rest.issues.createComment({
               owner: context.repo.owner,

.github/workflows/gemini-scheduled-issue-triage.yml

@@ -49,7 +49,7 @@ jobs:
 
           echo '🏷️ Finding issues that need triage...'
           NEED_TRIAGE_ISSUES="$(gh issue list --repo "${GITHUB_REPOSITORY}" \
-            --search 'is:open is:issue label:"status/needs-triage"' --json number,title,body)"
+            --search "is:open is:issue label:\"status/need-triage\""  --limit 1000 --json number,title,body)"
 
           echo '🔄 Merging and deduplicating issues...'
           ISSUES="$(echo "${NO_LABEL_ISSUES}" "${NEED_TRIAGE_ISSUES}" | jq -c -s 'add | unique_by(.number)')"
@@ -64,7 +64,7 @@ jobs:
         id: 'get_labels'
         uses: 'actions/github-script@60a0d83039c74a4aee543508d2ffcb1c3799cdea'
         with:
-          github-token: '${{ steps.generate_token.outputs.token || secrets.GITHUB_TOKEN }}'
+          github-token: '${{ steps.generate_token.outputs.token }}'
           script: |-
             const { data: labels } = await github.rest.issues.listLabelsForRepo({
               owner: context.repo.owner,
@@ -113,11 +113,13 @@ jobs:
 
             ## Steps
 
-            1. Review the available labels in the environment variable: "${AVAILABLE_LABELS}".
+            1. You are only able to use the echo command. Review the available labels in the environment variable: "${AVAILABLE_LABELS}".
             2. Check environment variable for issues to triage: $ISSUES_TO_TRIAGE (JSON array of issues)
             3. Review the issue title, body and any comments provided in the environment variables.
-            4. Ignore any existing priorities or tags on the issue.
-            5. Identify the most relevant labels from the existing labels, focusing on kind/*, area/*, sub-area/* and priority/*.
+            4. Identify the most relevant labels from the existing labels, focusing on kind/*, area/*, sub-area/* and priority/*.
+            5. If the issue already has area/ label, dont try to change it. Similarly, if the issue already has a kind/ label don't change it. And if the issue already has a priority/ label do not change it for example:
+               If an issue has area/core and kind/bug  you will only add a priority/ label.
+               Instead if an issue has no labels, you will could add one lable of each kind.
             6. Identify other applicable labels based on the issue content, such as status/*, help wanted, good first issue, etc.
             7. For area/* and kind/* limit yourself to only the single most applicable label in each case.
             8. Give me a single short explanation about why you are selecting each label in the process.
@@ -128,7 +130,7 @@ jobs:
                  {
                    "issue_number": 123,
                    "labels_to_add": ["kind/bug", "priority/p2"],
-                   "labels_to_remove": ["status/needs-triage"],
+                   "labels_to_remove": ["status/need-triage"],
                    "explanation": "This issue is a bug that needs to be addressed with medium priority."
                  },
                  {
@@ -142,8 +144,10 @@ jobs:
               If an issue cannot be classified, do not include it in the output array.
             10. For each issue please check if CLI version is present, this is usually in the output of the /about command and will look like 0.1.5
               - Anything more than 6 versions older than the most recent should add the status/need-retesting label
-            11. If you see that the issue doesn't look like it has sufficient information recommend the status/need-information label
+            11. If you see that the issue doesn't look like it has sufficient information recommend the status/need-information label and leave a comment politely requesting the relevant information, eg.. if repro steps are missing request for repro steps. if version information is missing request for version information into the explanation section below.
               - After identifying appropriate labels to an issue, add "status/need-triage" label to labels_to_remove in the output.
+            12. If you think an issue might be a Priority/P0 do not apply the priority/p0 label. Instead apply a status/manual-triage label and include a note in your explanation.
+            13. If you are uncertain and have not been able to apply one each of kind/, area/ and priority/ , apply the status/manual-triage label.
 
             ## Guidelines
 
@@ -151,7 +155,7 @@ jobs:
             - Do not include any explanation or additional text, just the JSON
             - Only use labels that already exist in the repository.
               - Do not add comments or modify the issue content.
-              - Do not remove labels titled help wanted or good first issue.
+              - Do not remove the following labels maintainer, help wanted or good first issue.
               - Triage only the current issue.
               - Identify only one area/ label
               - Identify only one kind/ label (Do not apply kind/duplicate or kind/parent-issue)
@@ -159,8 +163,11 @@ jobs:
               - Once you categorize the issue if it needs information bump down the priority by 1 eg.. a p0 would become a p1 a p1 would become a p2. P2 and P3 can stay as is in this scenario.
             Categorization Guidelines:
             P0: Critical / Blocker
-              - A P0 bug is a catastrophic failure that demands immediate attention. It represents a complete showstopper for a significant portion of users or for the development process itself.
-              Impact:
+              - A P0 bug is a catastrophic failure that demands immediate attention.
+              - To be a P0 it means almost all users are running into this issue and it is blocking users from being able to use the product.
+              - You would see this in the form of many comments from different developers on the bug.
+              - It represents a complete showstopper for a significant portion of users or for the development process itself.
+            Impact:
               - Blocks development or testing for the entire team.
               - Major security vulnerability that could compromise user data or system integrity.
               - Causes data loss or corruption with no workaround.
@@ -169,15 +176,17 @@ jobs:
               Qualifier: Is the main function of the software broken?
               Example: The gemini auth login command fails with an unrecoverable error, preventing any user from authenticating and using the rest of the CLI.
             P1: High
-              - A P1 bug is a serious issue that significantly degrades the user experience or impacts a core feature. While not a complete blocker, it's a major problem that needs a fast resolution.
-              - Feature requests are almost never P1.
+              - A P1 bug is a serious issue that significantly degrades the user experience or impacts a core feature.
+              - While not a complete blocker, it's a major problem that needs a fast resolution. Feature requests are almost never P1.
+              - Once again this would be affecting many users.
+              - You would see this in the form of comments from different developers on the bug.
               Impact:
               - A core feature is broken or behaving incorrectly for a large number of users or large number of use cases.
               - Review the bug details and comments to try figure out if this issue affects a large set of use cases or if it's a narrow set of use cases.
               - Severe performance degradation making the application frustratingly slow.
               - No straightforward workaround exists, or the workaround is difficult and non-obvious.
               Qualifier: Is a key feature unusable or giving very wrong results?
-              Example: The gemini -p "..." command consistently returns a malformed JSON response or an empty result, making the CLI's primary generation feature unreliable.
+              Example: Gemini CLI enters a loop when making read-many-files tool call. I am unable to break out of the loop and gemini doesn't follow instructions subsequently.
             P2: Medium
               - A P2 bug is a moderately impactful issue. It's a noticeable problem but doesn't prevent the use of the software's main functionality.
               Impact:
@@ -252,15 +261,18 @@ jobs:
           LABELS_OUTPUT: '${{ steps.gemini_issue_analysis.outputs.summary }}'
         uses: 'actions/github-script@60a0d83039c74a4aee543508d2ffcb1c3799cdea'
         with:
-          github-token: '${{ steps.generate_token.outputs.token || secrets.GITHUB_TOKEN }}'
+          github-token: '${{ steps.generate_token.outputs.token }}'
           script: |-
-            // Strip code block markers if present
             const rawLabels = process.env.LABELS_OUTPUT;
             core.info(`Raw labels JSON: ${rawLabels}`);
             let parsedLabels;
             try {
-              const trimmedLabels = rawLabels.replace(/^```(?:json)?\s*/, '').replace(/\s*```$/, '').trim();
-              parsedLabels = JSON.parse(trimmedLabels);
+              const jsonMatch = rawLabels.match(/```json\s*([\s\S]*?)\s*```/);
+              if (!jsonMatch || !jsonMatch[1]) {
+                throw new Error("Could not find a ```json ... ``` block in the output.");
+              }
+              const jsonString = jsonMatch[1].trim();
+              parsedLabels = JSON.parse(jsonString);
               core.info(`Parsed labels JSON: ${JSON.stringify(parsedLabels)}`);
             } catch (err) {
               core.setFailed(`Failed to parse labels JSON from Gemini output: ${err.message}\nRaw output: ${rawLabels}`);
@@ -274,18 +286,48 @@ jobs:
                 continue;
               }
 
-              // Set labels based on triage result
-              if (entry.labels_to_set && entry.labels_to_set.length > 0) {
-                await github.rest.issues.setLabels({
+              const labelsToAdd = entry.labels_to_add || [];
+              labelsToAdd.push('status/bot-triaged');
+
+              if (labelsToAdd.length > 0) {
+                await github.rest.issues.addLabels({
                   owner: context.repo.owner,
                   repo: context.repo.repo,
                   issue_number: issueNumber,
-                  labels: entry.labels_to_set
+                  labels: labelsToAdd
                 });
                 const explanation = entry.explanation ? ` - ${entry.explanation}` : '';
-                core.info(`Successfully set labels for #${issueNumber}: ${entry.labels_to_set.join(', ')}${explanation}`);
-              } else {
-                // If no labels to set, leave the issue as is
-                core.info(`No labels to set for #${issueNumber}, leaving as is`);
+                core.info(`Successfully added labels for #${issueNumber}: ${labelsToAdd.join(', ')}${explanation}`);
+              }
+
+              if (entry.labels_to_remove && entry.labels_to_remove.length > 0) {
+                for (const label of entry.labels_to_remove) {
+                  try {
+                    await github.rest.issues.removeLabel({
+                      owner: context.repo.owner,
+                      repo: context.repo.repo,
+                      issue_number: issueNumber,
+                      name: label
+                    });
+                  } catch (error) {
+                    if (error.status !== 404) {
+                      throw error;
+                    }
+                  }
+                }
+                core.info(`Successfully removed labels for #${issueNumber}: ${entry.labels_to_remove.join(', ')}`);
+              }
+
+              if (entry.explanation) {
+                await github.rest.issues.createComment({
+                  owner: context.repo.owner,
+                  repo: context.repo.repo,
+                  issue_number: issueNumber,
+                  body: entry.explanation,
+                });
+              }
+
+              if ((!entry.labels_to_add || entry.labels_to_add.length === 0) && (!entry.labels_to_remove || entry.labels_to_remove.length === 0)) {
+                core.info(`No labels to add or remove for #${issueNumber}, leaving as is`);
               }
             }

.github/workflows/gemini-self-assign-issue.yml

@@ -50,7 +50,8 @@ jobs:
 
             // Search for open issues already assigned to the commenter in this repo
             const { data: assignedIssues } = await github.rest.search.issuesAndPullRequests({
-              q: `is:issue repo:${owner}/${repo} assignee:${commenter} is:open`
+              q: `is:issue repo:${owner}/${repo} assignee:${commenter} is:open`,
+              advanced_search: true
             });
 
             if (assignedIssues.total_count >= MAX_ISSUES_ASSIGNED) {

.github/workflows/release.yml

@@ -228,4 +228,4 @@ jobs:
           gh issue create \
             --title "Release Failed for ${RELEASE_TAG} on $(date +'%Y-%m-%d')" \
             --body "The release workflow failed. See the full run for details: ${DETAILS_URL}" \
-            --label "kind/bug,release-failure"
+            --label "kind/bug,release-failure,priority/p0"

.gitignore

@@ -3,8 +3,14 @@
 .env~
 
 # gemini-cli settings
-.gemini/
-!gemini/config.yaml
+# We want to keep the .gemini in the root of the repo and ignore any .gemini
+# in subdirectories. In our root .gemini we want to allow for version control
+# for subcommands.
+**/.gemini/
+!/.gemini/
+.gemini/*
+!.gemini/config.yaml
+!.gemini/commands/
 
 # Note: .gemini-clipboard/ is NOT in gitignore so Gemini can access pasted images
 

CONTRIBUTING.md

@@ -31,6 +31,14 @@ All submissions, including submissions by project members, require review. We
 use [GitHub pull requests](https://docs.github.com/articles/about-pull-requests)
 for this purpose.
 
+### Self Assigning Issues
+
+If you're looking for an issue to work on, check out our list of issues that are labeled ["help wanted"](https://github.com/google-gemini/gemini-cli/issues?q=is%3Aissue+state%3Aopen+label%3A%22help+wanted%22).
+
+To assign an issue to yourself, simply add a comment with the text `/assign`. The comment must contain only that text and nothing else. This command will assign the issue to you, provided it is not already assigned.
+
+Please note that you can have a maximum of 3 issues assigned to you at any given time.
+
 ### Pull Request Guidelines
 
 To help us review and merge your PRs quickly, please follow these guidelines. PRs that do not meet these standards may be closed.

docs/checkpointing.md

@@ -38,8 +38,10 @@ Add the following key to your `settings.json`:
 
 ```json
 {
-  "checkpointing": {
-    "enabled": true
+  "general": {
+    "checkpointing": {
+      "enabled": true
+    }
   }
 }
 ```

docs/cli/commands.md

@@ -9,7 +9,7 @@ Slash commands provide meta-level control over the CLI itself.
 ### Built-in Commands
 
 - **`/bug`**
-  - **Description:** File an issue about Gemini CLI. By default, the issue is filed within the GitHub repository for Gemini CLI. The string you enter after `/bug` will become the headline for the bug being filed. The default `/bug` behavior can be modified using the `bugCommand` setting in your `.gemini/settings.json` files.
+  - **Description:** File an issue about Gemini CLI. By default, the issue is filed within the GitHub repository for Gemini CLI. The string you enter after `/bug` will become the headline for the bug being filed. The default `/bug` behavior can be modified using the `advanced.bugCommand` setting in your `.gemini/settings.json` files.
 
 - **`/chat`**
   - **Description:** Save and resume conversation history for branching conversation state interactively, or resuming a previous state from a later session.
@@ -395,7 +395,7 @@ At commands are used to include the content of files or directories as part of y
     - If a path to a directory is provided, the command attempts to read the content of files within that directory and any subdirectories.
     - Spaces in paths should be escaped with a backslash (e.g., `@My\ Documents/file.txt`).
     - The command uses the `read_many_files` tool internally. The content is fetched and then inserted into your query before being sent to the Gemini model.
-    - **Git-aware filtering:** By default, git-ignored files (like `node_modules/`, `dist/`, `.env`, `.git/`) are excluded. This behavior can be changed via the `fileFiltering` settings.
+    - **Git-aware filtering:** By default, git-ignored files (like `node_modules/`, `dist/`, `.env`, `.git/`) are excluded. This behavior can be changed via the `context.fileFiltering` settings.
     - **File types:** The command is intended for text-based files. While it might attempt to read any file, binary files or very large files might be skipped or truncated by the underlying `read_many_files` tool to ensure performance and relevance. The tool indicates if files were skipped.
   - **Output:** The CLI will show a tool call message indicating that `read_many_files` was used, along with a message detailing the status and the path(s) that were processed.
 

docs/cli/configuration-v1.md

@@ -0,0 +1,643 @@
+# Gemini CLI Configuration
+
+**Note on Deprecated Configuration Format**
+
+This document describes the legacy v1 format for the `settings.json` file. This format is now deprecated.
+
+- The new format will be supported in the stable release starting **[09/10/25]**.
+- Automatic migration from the old format to the new format will begin on **[09/17/25]**.
+
+For details on the new, recommended format, please see the [current Configuration documentation](./configuration.md).
+
+Gemini CLI offers several ways to configure its behavior, including environment variables, command-line arguments, and settings files. This document outlines the different configuration methods and available settings.
+
+## Configuration layers
+
+Configuration is applied in the following order of precedence (lower numbers are overridden by higher numbers):
+
+1.  **Default values:** Hardcoded defaults within the application.
+2.  **System defaults file:** System-wide default settings that can be overridden by other settings files.
+3.  **User settings file:** Global settings for the current user.
+4.  **Project settings file:** Project-specific settings.
+5.  **System settings file:** System-wide settings that override all other settings files.
+6.  **Environment variables:** System-wide or session-specific variables, potentially loaded from `.env` files.
+7.  **Command-line arguments:** Values passed when launching the CLI.
+
+## Settings files
+
+Gemini CLI uses JSON settings files for persistent configuration. There are four locations for these files:
+
+- **System defaults file:**
+  - **Location:** `/etc/gemini-cli/system-defaults.json` (Linux), `C:\ProgramData\gemini-cli\system-defaults.json` (Windows) or `/Library/Application Support/GeminiCli/system-defaults.json` (macOS). The path can be overridden using the `GEMINI_CLI_SYSTEM_DEFAULTS_PATH` environment variable.
+  - **Scope:** Provides a base layer of system-wide default settings. These settings have the lowest precedence and are intended to be overridden by user, project, or system override settings.
+- **User settings file:**
+  - **Location:** `~/.gemini/settings.json` (where `~` is your home directory).
+  - **Scope:** Applies to all Gemini CLI sessions for the current user. User settings override system defaults.
+- **Project settings file:**
+  - **Location:** `.gemini/settings.json` within your project's root directory.
+  - **Scope:** Applies only when running Gemini CLI from that specific project. Project settings override user settings and system defaults.
+- **System settings file:**
+  - **Location:** `/etc/gemini-cli/settings.json` (Linux), `C:\ProgramData\gemini-cli\settings.json` (Windows) or `/Library/Application Support/GeminiCli/settings.json` (macOS). The path can be overridden using the `GEMINI_CLI_SYSTEM_SETTINGS_PATH` environment variable.
+  - **Scope:** Applies to all Gemini CLI sessions on the system, for all users. System settings act as overrides, taking precedence over all other settings files. May be useful for system administrators at enterprises to have controls over users' Gemini CLI setups.
+
+**Note on environment variables in settings:** String values within your `settings.json` files can reference environment variables using either `$VAR_NAME` or `${VAR_NAME}` syntax. These variables will be automatically resolved when the settings are loaded. For example, if you have an environment variable `MY_API_TOKEN`, you could use it in `settings.json` like this: `"apiKey": "$MY_API_TOKEN"`.
+
+> **Note for Enterprise Users:** For guidance on deploying and managing Gemini CLI in a corporate environment, please see the [Enterprise Configuration](./enterprise.md) documentation.
+
+### The `.gemini` directory in your project
+
+In addition to a project settings file, a project's `.gemini` directory can contain other project-specific files related to Gemini CLI's operation, such as:
+
+- [Custom sandbox profiles](#sandboxing) (e.g., `.gemini/sandbox-macos-custom.sb`, `.gemini/sandbox.Dockerfile`).
+
+### Available settings in `settings.json`:
+
+- **`contextFileName`** (string or array of strings):
+  - **Description:** Specifies the filename for context files (e.g., `GEMINI.md`, `AGENTS.md`). Can be a single filename or a list of accepted filenames.
+  - **Default:** `GEMINI.md`
+  - **Example:** `"contextFileName": "AGENTS.md"`
+
+- **`bugCommand`** (object):
+  - **Description:** Overrides the default URL for the `/bug` command.
+  - **Default:** `"urlTemplate": "https://github.com/google-gemini/gemini-cli/issues/new?template=bug_report.yml&title={title}&info={info}"`
+  - **Properties:**
+    - **`urlTemplate`** (string): A URL that can contain `{title}` and `{info}` placeholders.
+  - **Example:**
+    ```json
+    "bugCommand": {
+      "urlTemplate": "https://bug.example.com/new?title={title}&info={info}"
+    }
+    ```
+
+- **`fileFiltering`** (object):
+  - **Description:** Controls git-aware file filtering behavior for @ commands and file discovery tools.
+  - **Default:** `"respectGitIgnore": true, "enableRecursiveFileSearch": true`
+  - **Properties:**
+    - **`respectGitIgnore`** (boolean): Whether to respect .gitignore patterns when discovering files. When set to `true`, git-ignored files (like `node_modules/`, `dist/`, `.env`) are automatically excluded from @ commands and file listing operations.
+    - **`enableRecursiveFileSearch`** (boolean): Whether to enable searching recursively for filenames under the current tree when completing @ prefixes in the prompt.
+    - **`disableFuzzySearch`** (boolean): When `true`, disables the fuzzy search capabilities when searching for files, which can improve performance on projects with a large number of files.
+  - **Example:**
+    ```json
+    "fileFiltering": {
+      "respectGitIgnore": true,
+      "enableRecursiveFileSearch": false,
+      "disableFuzzySearch": true
+    }
+    ```
+
+### Troubleshooting File Search Performance
+
+If you are experiencing performance issues with file searching (e.g., with `@` completions), especially in projects with a very large number of files, here are a few things you can try in order of recommendation:
+
+1.  **Use `.geminiignore`:** Create a `.geminiignore` file in your project root to exclude directories that contain a large number of files that you don't need to reference (e.g., build artifacts, logs, `node_modules`). Reducing the total number of files crawled is the most effective way to improve performance.
+
+2.  **Disable Fuzzy Search:** If ignoring files is not enough, you can disable fuzzy search by setting `disableFuzzySearch` to `true` in your `settings.json` file. This will use a simpler, non-fuzzy matching algorithm, which can be faster.
+
+3.  **Disable Recursive File Search:** As a last resort, you can disable recursive file search entirely by setting `enableRecursiveFileSearch` to `false`. This will be the fastest option as it avoids a recursive crawl of your project. However, it means you will need to type the full path to files when using `@` completions.
+
+- **`coreTools`** (array of strings):
+  - **Description:** Allows you to specify a list of core tool names that should be made available to the model. This can be used to restrict the set of built-in tools. See [Built-in Tools](../core/tools-api.md#built-in-tools) for a list of core tools. You can also specify command-specific restrictions for tools that support it, like the `ShellTool`. For example, `"coreTools": ["ShellTool(ls -l)"]` will only allow the `ls -l` command to be executed.
+  - **Default:** All tools available for use by the Gemini model.
+  - **Example:** `"coreTools": ["ReadFileTool", "GlobTool", "ShellTool(ls)"]`.
+
+- **`allowedTools`** (array of strings):
+  - **Default:** `undefined`
+  - **Description:** A list of tool names that will bypass the confirmation dialog. This is useful for tools that you trust and use frequently. The match semantics are the same as `coreTools`.
+  - **Example:** `"allowedTools": ["ShellTool(git status)"]`.
+
+- **`excludeTools`** (array of strings):
+  - **Description:** Allows you to specify a list of core tool names that should be excluded from the model. A tool listed in both `excludeTools` and `coreTools` is excluded. You can also specify command-specific restrictions for tools that support it, like the `ShellTool`. For example, `"excludeTools": ["ShellTool(rm -rf)"]` will block the `rm -rf` command.
+  - **Default**: No tools excluded.
+  - **Example:** `"excludeTools": ["run_shell_command", "findFiles"]`.
+  - **Security Note:** Command-specific restrictions in
+    `excludeTools` for `run_shell_command` are based on simple string matching and can be easily bypassed. This feature is **not a security mechanism** and should not be relied upon to safely execute untrusted code. It is recommended to use `coreTools` to explicitly select commands
+    that can be executed.
+
+- **`allowMCPServers`** (array of strings):
+  - **Description:** Allows you to specify a list of MCP server names that should be made available to the model. This can be used to restrict the set of MCP servers to connect to. Note that this will be ignored if `--allowed-mcp-server-names` is set.
+  - **Default:** All MCP servers are available for use by the Gemini model.
+  - **Example:** `"allowMCPServers": ["myPythonServer"]`.
+  - **Security Note:** This uses simple string matching on MCP server names, which can be modified. If you're a system administrator looking to prevent users from bypassing this, consider configuring the `mcpServers` at the system settings level such that the user will not be able to configure any MCP servers of their own. This should not be used as an airtight security mechanism.
+
+- **`excludeMCPServers`** (array of strings):
+  - **Description:** Allows you to specify a list of MCP server names that should be excluded from the model. A server listed in both `excludeMCPServers` and `allowMCPServers` is excluded. Note that this will be ignored if `--allowed-mcp-server-names` is set.
+  - **Default**: No MCP servers excluded.
+  - **Example:** `"excludeMCPServers": ["myNodeServer"]`.
+  - **Security Note:** This uses simple string matching on MCP server names, which can be modified. If you're a system administrator looking to prevent users from bypassing this, consider configuring the `mcpServers` at the system settings level such that the user will not be able to configure any MCP servers of their own. This should not be used as an airtight security mechanism.
+
+- **`autoAccept`** (boolean):
+  - **Description:** Controls whether the CLI automatically accepts and executes tool calls that are considered safe (e.g., read-only operations) without explicit user confirmation. If set to `true`, the CLI will bypass the confirmation prompt for tools deemed safe.
+  - **Default:** `false`
+  - **Example:** `"autoAccept": true`
+
+- **`theme`** (string):
+  - **Description:** Sets the visual [theme](./themes.md) for Gemini CLI.
+  - **Default:** `"Default"`
+  - **Example:** `"theme": "GitHub"`
+
+- **`vimMode`** (boolean):
+  - **Description:** Enables or disables vim mode for input editing. When enabled, the input area supports vim-style navigation and editing commands with NORMAL and INSERT modes. The vim mode status is displayed in the footer and persists between sessions.
+  - **Default:** `false`
+  - **Example:** `"vimMode": true`
+
+- **`sandbox`** (boolean or string):
+  - **Description:** Controls whether and how to use sandboxing for tool execution. If set to `true`, Gemini CLI uses a pre-built `gemini-cli-sandbox` Docker image. For more information, see [Sandboxing](#sandboxing).
+  - **Default:** `false`
+  - **Example:** `"sandbox": "docker"`
+
+- **`toolDiscoveryCommand`** (string):
+  - **Description:** Defines a custom shell command for discovering tools from your project. The shell command must return on `stdout` a JSON array of [function declarations](https://ai.google.dev/gemini-api/docs/function-calling#function-declarations). Tool wrappers are optional.
+  - **Default:** Empty
+  - **Example:** `"toolDiscoveryCommand": "bin/get_tools"`
+
+- **`toolCallCommand`** (string):
+  - **Description:** Defines a custom shell command for calling a specific tool that was discovered using `toolDiscoveryCommand`. The shell command must meet the following criteria:
+    - It must take function `name` (exactly as in [function declaration](https://ai.google.dev/gemini-api/docs/function-calling#function-declarations)) as first command line argument.
+    - It must read function arguments as JSON on `stdin`, analogous to [`functionCall.args`](https://cloud.google.com/vertex-ai/generative-ai/docs/model-reference/inference#functioncall).
+    - It must return function output as JSON on `stdout`, analogous to [`functionResponse.response.content`](https://cloud.google.com/vertex-ai/generative-ai/docs/model-reference/inference#functionresponse).
+  - **Default:** Empty
+  - **Example:** `"toolCallCommand": "bin/call_tool"`
+
+- **`mcpServers`** (object):
+  - **Description:** Configures connections to one or more Model-Context Protocol (MCP) servers for discovering and using custom tools. Gemini CLI attempts to connect to each configured MCP server to discover available tools. If multiple MCP servers expose a tool with the same name, the tool names will be prefixed with the server alias you defined in the configuration (e.g., `serverAlias__actualToolName`) to avoid conflicts. Note that the system might strip certain schema properties from MCP tool definitions for compatibility. At least one of `command`, `url`, or `httpUrl` must be provided. If multiple are specified, the order of precedence is `httpUrl`, then `url`, then `command`.
+  - **Default:** Empty
+  - **Properties:**
+    - **`<SERVER_NAME>`** (object): The server parameters for the named server.
+      - `command` (string, optional): The command to execute to start the MCP server via standard I/O.
+      - `args` (array of strings, optional): Arguments to pass to the command.
+      - `env` (object, optional): Environment variables to set for the server process.
+      - `cwd` (string, optional): The working directory in which to start the server.
+      - `url` (string, optional): The URL of an MCP server that uses Server-Sent Events (SSE) for communication.
+      - `httpUrl` (string, optional): The URL of an MCP server that uses streamable HTTP for communication.
+      - `headers` (object, optional): A map of HTTP headers to send with requests to `url` or `httpUrl`.
+      - `timeout` (number, optional): Timeout in milliseconds for requests to this MCP server.
+      - `trust` (boolean, optional): Trust this server and bypass all tool call confirmations.
+      - `description` (string, optional): A brief description of the server, which may be used for display purposes.
+      - `includeTools` (array of strings, optional): List of tool names to include from this MCP server. When specified, only the tools listed here will be available from this server (allowlist behavior). If not specified, all tools from the server are enabled by default.
+      - `excludeTools` (array of strings, optional): List of tool names to exclude from this MCP server. Tools listed here will not be available to the model, even if they are exposed by the server. **Note:** `excludeTools` takes precedence over `includeTools` - if a tool is in both lists, it will be excluded.
+  - **Example:**
+    ```json
+    "mcpServers": {
+      "myPythonServer": {
+        "command": "python",
+        "args": ["mcp_server.py", "--port", "8080"],
+        "cwd": "./mcp_tools/python",
+        "timeout": 5000,
+        "includeTools": ["safe_tool", "file_reader"],
+      },
+      "myNodeServer": {
+        "command": "node",
+        "args": ["mcp_server.js"],
+        "cwd": "./mcp_tools/node",
+        "excludeTools": ["dangerous_tool", "file_deleter"]
+      },
+      "myDockerServer": {
+        "command": "docker",
+        "args": ["run", "-i", "--rm", "-e", "API_KEY", "ghcr.io/foo/bar"],
+        "env": {
+          "API_KEY": "$MY_API_TOKEN"
+        }
+      },
+      "mySseServer": {
+        "url": "http://localhost:8081/events",
+        "headers": {
+          "Authorization": "Bearer $MY_SSE_TOKEN"
+        },
+        "description": "An example SSE-based MCP server."
+      },
+      "myStreamableHttpServer": {
+        "httpUrl": "http://localhost:8082/stream",
+        "headers": {
+          "X-API-Key": "$MY_HTTP_API_KEY"
+        },
+        "description": "An example Streamable HTTP-based MCP server."
+      }
+    }
+    ```
+
+- **`checkpointing`** (object):
+  - **Description:** Configures the checkpointing feature, which allows you to save and restore conversation and file states. See the [Checkpointing documentation](../checkpointing.md) for more details.
+  - **Default:** `{"enabled": false}`
+  - **Properties:**
+    - **`enabled`** (boolean): When `true`, the `/restore` command is available.
+
+- **`preferredEditor`** (string):
+  - **Description:** Specifies the preferred editor to use for viewing diffs.
+  - **Default:** `vscode`
+  - **Example:** `"preferredEditor": "vscode"`
+
+- **`telemetry`** (object)
+  - **Description:** Configures logging and metrics collection for Gemini CLI. For more information, see [Telemetry](../telemetry.md).
+  - **Default:** `{"enabled": false, "target": "local", "otlpEndpoint": "http://localhost:4317", "logPrompts": true}`
+  - **Properties:**
+    - **`enabled`** (boolean): Whether or not telemetry is enabled.
+    - **`target`** (string): The destination for collected telemetry. Supported values are `local` and `gcp`.
+    - **`otlpEndpoint`** (string): The endpoint for the OTLP Exporter.
+    - **`logPrompts`** (boolean): Whether or not to include the content of user prompts in the logs.
+  - **Example:**
+    ```json
+    "telemetry": {
+      "enabled": true,
+      "target": "local",
+      "otlpEndpoint": "http://localhost:16686",
+      "logPrompts": false
+    }
+    ```
+- **`usageStatisticsEnabled`** (boolean):
+  - **Description:** Enables or disables the collection of usage statistics. See [Usage Statistics](#usage-statistics) for more information.
+  - **Default:** `true`
+  - **Example:**
+    ```json
+    "usageStatisticsEnabled": false
+    ```
+
+- **`hideTips`** (boolean):
+  - **Description:** Enables or disables helpful tips in the CLI interface.
+  - **Default:** `false`
+  - **Example:**
+
+    ```json
+    "hideTips": true
+    ```
+
+- **`hideBanner`** (boolean):
+  - **Description:** Enables or disables the startup banner (ASCII art logo) in the CLI interface.
+  - **Default:** `false`
+  - **Example:**
+
+    ```json
+    "hideBanner": true
+    ```
+
+- **`maxSessionTurns`** (number):
+  - **Description:** Sets the maximum number of turns for a session. If the session exceeds this limit, the CLI will stop processing and start a new chat.
+  - **Default:** `-1` (unlimited)
+  - **Example:**
+    ```json
+    "maxSessionTurns": 10
+    ```
+
+- **`summarizeToolOutput`** (object):
+  - **Description:** Enables or disables the summarization of tool output. You can specify the token budget for the summarization using the `tokenBudget` setting.
+  - Note: Currently only the `run_shell_command` tool is supported.
+  - **Default:** `{}` (Disabled by default)
+  - **Example:**
+    ```json
+    "summarizeToolOutput": {
+      "run_shell_command": {
+        "tokenBudget": 2000
+      }
+    }
+    ```
+
+- **`excludedProjectEnvVars`** (array of strings):
+  - **Description:** Specifies environment variables that should be excluded from being loaded from project `.env` files. This prevents project-specific environment variables (like `DEBUG=true`) from interfering with gemini-cli behavior. Variables from `.gemini/.env` files are never excluded.
+  - **Default:** `["DEBUG", "DEBUG_MODE"]`
+  - **Example:**
+    ```json
+    "excludedProjectEnvVars": ["DEBUG", "DEBUG_MODE", "NODE_ENV"]
+    ```
+
+- **`includeDirectories`** (array of strings):
+  - **Description:** Specifies an array of additional absolute or relative paths to include in the workspace context. Missing directories will be skipped with a warning by default. Paths can use `~` to refer to the user's home directory. This setting can be combined with the `--include-directories` command-line flag.
+  - **Default:** `[]`
+  - **Example:**
+    ```json
+    "includeDirectories": [
+      "/path/to/another/project",
+      "../shared-library",
+      "~/common-utils"
+    ]
+    ```
+
+- **`loadMemoryFromIncludeDirectories`** (boolean):
+  - **Description:** Controls the behavior of the `/memory refresh` command. If set to `true`, `GEMINI.md` files should be loaded from all directories that are added. If set to `false`, `GEMINI.md` should only be loaded from the current directory.
+  - **Default:** `false`
+  - **Example:**
+    ```json
+    "loadMemoryFromIncludeDirectories": true
+    ```
+
+- **`chatCompression`** (object):
+  - **Description:** Controls the settings for chat history compression, both automatic and
+    when manually invoked through the /compress command.
+  - **Properties:**
+    - **`contextPercentageThreshold`** (number): A value between 0 and 1 that specifies the token threshold for compression as a percentage of the model's total token limit. For example, a value of `0.6` will trigger compression when the chat history exceeds 60% of the token limit.
+  - **Example:**
+    ```json
+    "chatCompression": {
+      "contextPercentageThreshold": 0.6
+    }
+    ```
+
+- **`showLineNumbers`** (boolean):
+  - **Description:** Controls whether line numbers are displayed in code blocks in the CLI output.
+  - **Default:** `true`
+  - **Example:**
+    ```json
+    "showLineNumbers": false
+    ```
+
+- **`accessibility`** (object):
+  - **Description:** Configures accessibility features for the CLI.
+  - **Properties:**
+    - **`screenReader`** (boolean): Enables screen reader mode, which adjusts the TUI for better compatibility with screen readers. This can also be enabled with the `--screen-reader` command-line flag, which will take precedence over the setting.
+    - **`disableLoadingPhrases`** (boolean): Disables the display of loading phrases during operations.
+  - **Default:** `{"screenReader": false, "disableLoadingPhrases": false}`
+  - **Example:**
+    ```json
+    "accessibility": {
+      "screenReader": true,
+      "disableLoadingPhrases": true
+    }
+    ```
+
+### Example `settings.json`:
+
+```json
+{
+  "theme": "GitHub",
+  "sandbox": "docker",
+  "toolDiscoveryCommand": "bin/get_tools",
+  "toolCallCommand": "bin/call_tool",
+  "mcpServers": {
+    "mainServer": {
+      "command": "bin/mcp_server.py"
+    },
+    "anotherServer": {
+      "command": "node",
+      "args": ["mcp_server.js", "--verbose"]
+    }
+  },
+  "telemetry": {
+    "enabled": true,
+    "target": "local",
+    "otlpEndpoint": "http://localhost:4317",
+    "logPrompts": true
+  },
+  "usageStatisticsEnabled": true,
+  "hideTips": false,
+  "hideBanner": false,
+  "maxSessionTurns": 10,
+  "summarizeToolOutput": {
+    "run_shell_command": {
+      "tokenBudget": 100
+    }
+  },
+  "excludedProjectEnvVars": ["DEBUG", "DEBUG_MODE", "NODE_ENV"],
+  "includeDirectories": ["path/to/dir1", "~/path/to/dir2", "../path/to/dir3"],
+  "loadMemoryFromIncludeDirectories": true
+}
+```
+
+## Shell History
+
+The CLI keeps a history of shell commands you run. To avoid conflicts between different projects, this history is stored in a project-specific directory within your user's home folder.
+
+- **Location:** `~/.gemini/tmp/<project_hash>/shell_history`
+  - `<project_hash>` is a unique identifier generated from your project's root path.
+  - The history is stored in a file named `shell_history`.
+
+## Environment Variables & `.env` Files
+
+Environment variables are a common way to configure applications, especially for sensitive information like API keys or for settings that might change between environments. For authentication setup, see the [Authentication documentation](./authentication.md) which covers all available authentication methods.
+
+The CLI automatically loads environment variables from an `.env` file. The loading order is:
+
+1.  `.env` file in the current working directory.
+2.  If not found, it searches upwards in parent directories until it finds an `.env` file or reaches the project root (identified by a `.git` folder) or the home directory.
+3.  If still not found, it looks for `~/.env` (in the user's home directory).
+
+**Environment Variable Exclusion:** Some environment variables (like `DEBUG` and `DEBUG_MODE`) are automatically excluded from being loaded from project `.env` files to prevent interference with gemini-cli behavior. Variables from `.gemini/.env` files are never excluded. You can customize this behavior using the `excludedProjectEnvVars` setting in your `settings.json` file.
+
+- **`GEMINI_API_KEY`**:
+  - Your API key for the Gemini API.
+  - One of several available [authentication methods](./authentication.md).
+  - Set this in your shell profile (e.g., `~/.bashrc`, `~/.zshrc`) or an `.env` file.
+- **`GEMINI_MODEL`**:
+  - Specifies the default Gemini model to use.
+  - Overrides the hardcoded default
+  - Example: `export GEMINI_MODEL="gemini-2.5-flash"`
+- **`GOOGLE_API_KEY`**:
+  - Your Google Cloud API key.
+  - Required for using Vertex AI in express mode.
+  - Ensure you have the necessary permissions.
+  - Example: `export GOOGLE_API_KEY="YOUR_GOOGLE_API_KEY"`.
+- **`GOOGLE_CLOUD_PROJECT`**:
+  - Your Google Cloud Project ID.
+  - Required for using Code Assist or Vertex AI.
+  - If using Vertex AI, ensure you have the necessary permissions in this project.
+  - **Cloud Shell Note:** When running in a Cloud Shell environment, this variable defaults to a special project allocated for Cloud Shell users. If you have `GOOGLE_CLOUD_PROJECT` set in your global environment in Cloud Shell, it will be overridden by this default. To use a different project in Cloud Shell, you must define `GOOGLE_CLOUD_PROJECT` in a `.env` file.
+  - Example: `export GOOGLE_CLOUD_PROJECT="YOUR_PROJECT_ID"`.
+- **`GOOGLE_APPLICATION_CREDENTIALS`** (string):
+  - **Description:** The path to your Google Application Credentials JSON file.
+  - **Example:** `export GOOGLE_APPLICATION_CREDENTIALS="/path/to/your/credentials.json"`
+- **`OTLP_GOOGLE_CLOUD_PROJECT`**:
+  - Your Google Cloud Project ID for Telemetry in Google Cloud
+  - Example: `export OTLP_GOOGLE_CLOUD_PROJECT="YOUR_PROJECT_ID"`.
+- **`GOOGLE_CLOUD_LOCATION`**:
+  - Your Google Cloud Project Location (e.g., us-central1).
+  - Required for using Vertex AI in non express mode.
+  - Example: `export GOOGLE_CLOUD_LOCATION="YOUR_PROJECT_LOCATION"`.
+- **`GEMINI_SANDBOX`**:
+  - Alternative to the `sandbox` setting in `settings.json`.
+  - Accepts `true`, `false`, `docker`, `podman`, or a custom command string.
+- **`SEATBELT_PROFILE`** (macOS specific):
+  - Switches the Seatbelt (`sandbox-exec`) profile on macOS.
+  - `permissive-open`: (Default) Restricts writes to the project folder (and a few other folders, see `packages/cli/src/utils/sandbox-macos-permissive-open.sb`) but allows other operations.
+  - `strict`: Uses a strict profile that declines operations by default.
+  - `<profile_name>`: Uses a custom profile. To define a custom profile, create a file named `sandbox-macos-<profile_name>.sb` in your project's `.gemini/` directory (e.g., `my-project/.gemini/sandbox-macos-custom.sb`).
+- **`DEBUG` or `DEBUG_MODE`** (often used by underlying libraries or the CLI itself):
+  - Set to `true` or `1` to enable verbose debug logging, which can be helpful for troubleshooting.
+  - **Note:** These variables are automatically excluded from project `.env` files by default to prevent interference with gemini-cli behavior. Use `.gemini/.env` files if you need to set these for gemini-cli specifically.
+- **`NO_COLOR`**:
+  - Set to any value to disable all color output in the CLI.
+- **`CLI_TITLE`**:
+  - Set to a string to customize the title of the CLI.
+- **`CODE_ASSIST_ENDPOINT`**:
+  - Specifies the endpoint for the code assist server.
+  - This is useful for development and testing.
+
+## Command-Line Arguments
+
+Arguments passed directly when running the CLI can override other configurations for that specific session.
+
+- **`--model <model_name>`** (**`-m <model_name>`**):
+  - Specifies the Gemini model to use for this session.
+  - Example: `npm start -- --model gemini-1.5-pro-latest`
+- **`--prompt <your_prompt>`** (**`-p <your_prompt>`**):
+  - Used to pass a prompt directly to the command. This invokes Gemini CLI in a non-interactive mode.
+- **`--prompt-interactive <your_prompt>`** (**`-i <your_prompt>`**):
+  - Starts an interactive session with the provided prompt as the initial input.
+  - The prompt is processed within the interactive session, not before it.
+  - Cannot be used when piping input from stdin.
+  - Example: `gemini -i "explain this code"`
+- **`--sandbox`** (**`-s`**):
+  - Enables sandbox mode for this session.
+- **`--sandbox-image`**:
+  - Sets the sandbox image URI.
+- **`--debug`** (**`-d`**):
+  - Enables debug mode for this session, providing more verbose output.
+- **`--all-files`** (**`-a`**):
+  - If set, recursively includes all files within the current directory as context for the prompt.
+- **`--help`** (or **`-h`**):
+  - Displays help information about command-line arguments.
+- **`--show-memory-usage`**:
+  - Displays the current memory usage.
+- **`--yolo`**:
+  - Enables YOLO mode, which automatically approves all tool calls.
+- **`--approval-mode <mode>`**:
+  - Sets the approval mode for tool calls. Available modes:
+    - `default`: Prompt for approval on each tool call (default behavior)
+    - `auto_edit`: Automatically approve edit tools (replace, write_file) while prompting for others
+    - `yolo`: Automatically approve all tool calls (equivalent to `--yolo`)
+  - Cannot be used together with `--yolo`. Use `--approval-mode=yolo` instead of `--yolo` for the new unified approach.
+  - Example: `gemini --approval-mode auto_edit`
+- **`--allowed-tools <tool1,tool2,...>`**:
+  - A comma-separated list of tool names that will bypass the confirmation dialog.
+  - Example: `gemini --allowed-tools "ShellTool(git status)"`
+- **`--telemetry`**:
+  - Enables [telemetry](../telemetry.md).
+- **`--telemetry-target`**:
+  - Sets the telemetry target. See [telemetry](../telemetry.md) for more information.
+- **`--telemetry-otlp-endpoint`**:
+  - Sets the OTLP endpoint for telemetry. See [telemetry](../telemetry.md) for more information.
+- **`--telemetry-otlp-protocol`**:
+  - Sets the OTLP protocol for telemetry (`grpc` or `http`). Defaults to `grpc`. See [telemetry](../telemetry.md) for more information.
+- **`--telemetry-log-prompts`**:
+  - Enables logging of prompts for telemetry. See [telemetry](../telemetry.md) for more information.
+- **`--checkpointing`**:
+  - Enables [checkpointing](../checkpointing.md).
+- **`--extensions <extension_name ...>`** (**`-e <extension_name ...>`**):
+  - Specifies a list of extensions to use for the session. If not provided, all available extensions are used.
+  - Use the special term `gemini -e none` to disable all extensions.
+  - Example: `gemini -e my-extension -e my-other-extension`
+- **`--list-extensions`** (**`-l`**):
+  - Lists all available extensions and exits.
+- **`--proxy`**:
+  - Sets the proxy for the CLI.
+  - Example: `--proxy http://localhost:7890`.
+- **`--include-directories <dir1,dir2,...>`**:
+  - Includes additional directories in the workspace for multi-directory support.
+  - Can be specified multiple times or as comma-separated values.
+  - 5 directories can be added at maximum.
+  - Example: `--include-directories /path/to/project1,/path/to/project2` or `--include-directories /path/to/project1 --include-directories /path/to/project2`
+- **`--screen-reader`**:
+  - Enables screen reader mode for accessibility.
+- **`--version`**:
+  - Displays the version of the CLI.
+
+## Context Files (Hierarchical Instructional Context)
+
+While not strictly configuration for the CLI's _behavior_, context files (defaulting to `GEMINI.md` but configurable via the `contextFileName` setting) are crucial for configuring the _instructional context_ (also referred to as "memory") provided to the Gemini model. This powerful feature allows you to give project-specific instructions, coding style guides, or any relevant background information to the AI, making its responses more tailored and accurate to your needs. The CLI includes UI elements, such as an indicator in the footer showing the number of loaded context files, to keep you informed about the active context.
+
+- **Purpose:** These Markdown files contain instructions, guidelines, or context that you want the Gemini model to be aware of during your interactions. The system is designed to manage this instructional context hierarchically.
+
+### Example Context File Content (e.g., `GEMINI.md`)
+
+Here's a conceptual example of what a context file at the root of a TypeScript project might contain:
+
+```markdown
+# Project: My Awesome TypeScript Library
+
+## General Instructions:
+
+- When generating new TypeScript code, please follow the existing coding style.
+- Ensure all new functions and classes have JSDoc comments.
+- Prefer functional programming paradigms where appropriate.
+- All code should be compatible with TypeScript 5.0 and Node.js 20+.
+
+## Coding Style:
+
+- Use 2 spaces for indentation.
+- Interface names should be prefixed with `I` (e.g., `IUserService`).
+- Private class members should be prefixed with an underscore (`_`).
+- Always use strict equality (`===` and `!==`).
+
+## Specific Component: `src/api/client.ts`
+
+- This file handles all outbound API requests.
+- When adding new API call functions, ensure they include robust error handling and logging.
+- Use the existing `fetchWithRetry` utility for all GET requests.
+
+## Regarding Dependencies:
+
+- Avoid introducing new external dependencies unless absolutely necessary.
+- If a new dependency is required, please state the reason.
+```
+
+This example demonstrates how you can provide general project context, specific coding conventions, and even notes about particular files or components. The more relevant and precise your context files are, the better the AI can assist you. Project-specific context files are highly encouraged to establish conventions and context.
+
+- **Hierarchical Loading and Precedence:** The CLI implements a sophisticated hierarchical memory system by loading context files (e.g., `GEMINI.md`) from several locations. Content from files lower in this list (more specific) typically overrides or supplements content from files higher up (more general). The exact concatenation order and final context can be inspected using the `/memory show` command. The typical loading order is:
+  1.  **Global Context File:**
+      - Location: `~/.gemini/<contextFileName>` (e.g., `~/.gemini/GEMINI.md` in your user home directory).
+      - Scope: Provides default instructions for all your projects.
+  2.  **Project Root & Ancestors Context Files:**
+      - Location: The CLI searches for the configured context file in the current working directory and then in each parent directory up to either the project root (identified by a `.git` folder) or your home directory.
+      - Scope: Provides context relevant to the entire project or a significant portion of it.
+  3.  **Sub-directory Context Files (Contextual/Local):**
+      - Location: The CLI also scans for the configured context file in subdirectories _below_ the current working directory (respecting common ignore patterns like `node_modules`, `.git`, etc.). The breadth of this search is limited to 200 directories by default, but can be configured with a `memoryDiscoveryMaxDirs` field in your `settings.json` file.
+      - Scope: Allows for highly specific instructions relevant to a particular component, module, or subsection of your project.
+- **Concatenation & UI Indication:** The contents of all found context files are concatenated (with separators indicating their origin and path) and provided as part of the system prompt to the Gemini model. The CLI footer displays the count of loaded context files, giving you a quick visual cue about the active instructional context.
+- **Importing Content:** You can modularize your context files by importing other Markdown files using the `@path/to/file.md` syntax. For more details, see the [Memory Import Processor documentation](../core/memport.md).
+- **Commands for Memory Management:**
+  - Use `/memory refresh` to force a re-scan and reload of all context files from all configured locations. This updates the AI's instructional context.
+  - Use `/memory show` to display the combined instructional context currently loaded, allowing you to verify the hierarchy and content being used by the AI.
+  - See the [Commands documentation](./commands.md#memory) for full details on the `/memory` command and its sub-commands (`show` and `refresh`).
+
+By understanding and utilizing these configuration layers and the hierarchical nature of context files, you can effectively manage the AI's memory and tailor the Gemini CLI's responses to your specific needs and projects.
+
+## Sandboxing
+
+The Gemini CLI can execute potentially unsafe operations (like shell commands and file modifications) within a sandboxed environment to protect your system.
+
+Sandboxing is disabled by default, but you can enable it in a few ways:
+
+- Using `--sandbox` or `-s` flag.
+- Setting `GEMINI_SANDBOX` environment variable.
+- Sandbox is enabled when using `--yolo` or `--approval-mode=yolo` by default.
+
+By default, it uses a pre-built `gemini-cli-sandbox` Docker image.
+
+For project-specific sandboxing needs, you can create a custom Dockerfile at `.gemini/sandbox.Dockerfile` in your project's root directory. This Dockerfile can be based on the base sandbox image:
+
+```dockerfile
+FROM gemini-cli-sandbox
+
+# Add your custom dependencies or configurations here
+# For example:
+# RUN apt-get update && apt-get install -y some-package
+# COPY ./my-config /app/my-config
+```
+
+When `.gemini/sandbox.Dockerfile` exists, you can use `BUILD_SANDBOX` environment variable when running Gemini CLI to automatically build the custom sandbox image:
+
+```bash
+BUILD_SANDBOX=1 gemini -s
+```
+
+## Usage Statistics
+
+To help us improve the Gemini CLI, we collect anonymized usage statistics. This data helps us understand how the CLI is used, identify common issues, and prioritize new features.
+
+**What we collect:**
+
+- **Tool Calls:** We log the names of the tools that are called, whether they succeed or fail, and how long they take to execute. We do not collect the arguments passed to the tools or any data returned by them.
+- **API Requests:** We log the Gemini model used for each request, the duration of the request, and whether it was successful. We do not collect the content of the prompts or responses.
+- **Session Information:** We collect information about the configuration of the CLI, such as the enabled tools and the approval mode.
+
+**What we DON'T collect:**
+
+- **Personally Identifiable Information (PII):** We do not collect any personal information, such as your name, email address, or API keys.
+- **Prompt and Response Content:** We do not log the content of your prompts or the responses from the Gemini model.
+- **File Content:** We do not log the content of any files that are read or written by the CLI.
+
+**How to opt out:**
+
+You can opt out of usage statistics collection at any time by setting the `usageStatisticsEnabled` property to `false` in your `settings.json` file:
+
+```json
+{
+  "usageStatisticsEnabled": false
+}
+```

docs/cli/configuration.md

@@ -1,5 +1,14 @@
 # Gemini CLI Configuration
 
+**Note on New Configuration Format**
+
+The format of the `settings.json` file has been updated to a new, more organized structure.
+
+- The new format will be supported in the stable release starting **[09/10/25]**.
+- Automatic migration from the old format to the new format will begin on **[09/17/25]**.
+
+For details on the previous format, please see the [v1 Configuration documentation](./configuration-v1.md).
+
 Gemini CLI offers several ways to configure its behavior, including environment variables, command-line arguments, and settings files. This document outlines the different configuration methods and available settings.
 
 ## Configuration layers
@@ -41,316 +50,280 @@ In addition to a project settings file, a project's `.gemini` directory can cont
 
 - [Custom sandbox profiles](#sandboxing) (e.g., `.gemini/sandbox-macos-custom.sb`, `.gemini/sandbox.Dockerfile`).
 
-### Available settings in `settings.json`:
+### Available settings in `settings.json`
 
-- **`contextFileName`** (string or array of strings):
-  - **Description:** Specifies the filename for context files (e.g., `GEMINI.md`, `AGENTS.md`). Can be a single filename or a list of accepted filenames.
-  - **Default:** `GEMINI.md`
-  - **Example:** `"contextFileName": "AGENTS.md"`
+Settings are organized into categories. All settings should be placed within their corresponding top-level category object in your `settings.json` file.
 
-- **`bugCommand`** (object):
-  - **Description:** Overrides the default URL for the `/bug` command.
-  - **Default:** `"urlTemplate": "https://github.com/google-gemini/gemini-cli/issues/new?template=bug_report.yml&title={title}&info={info}"`
-  - **Properties:**
-    - **`urlTemplate`** (string): A URL that can contain `{title}` and `{info}` placeholders.
-  - **Example:**
-    ```json
-    "bugCommand": {
-      "urlTemplate": "https://bug.example.com/new?title={title}&info={info}"
-    }
-    ```
+#### `general`
 
-- **`fileFiltering`** (object):
-  - **Description:** Controls git-aware file filtering behavior for @ commands and file discovery tools.
-  - **Default:** `"respectGitIgnore": true, "enableRecursiveFileSearch": true`
-  - **Properties:**
-    - **`respectGitIgnore`** (boolean): Whether to respect .gitignore patterns when discovering files. When set to `true`, git-ignored files (like `node_modules/`, `dist/`, `.env`) are automatically excluded from @ commands and file listing operations.
-    - **`enableRecursiveFileSearch`** (boolean): Whether to enable searching recursively for filenames under the current tree when completing @ prefixes in the prompt.
-    - **`disableFuzzySearch`** (boolean): When `true`, disables the fuzzy search capabilities when searching for files, which can improve performance on projects with a large number of files.
-  - **Example:**
-    ```json
-    "fileFiltering": {
-      "respectGitIgnore": true,
-      "enableRecursiveFileSearch": false,
-      "disableFuzzySearch": true
-    }
-    ```
-
-### Troubleshooting File Search Performance
-
-If you are experiencing performance issues with file searching (e.g., with `@` completions), especially in projects with a very large number of files, here are a few things you can try in order of recommendation:
-
-1.  **Use `.geminiignore`:** Create a `.geminiignore` file in your project root to exclude directories that contain a large number of files that you don't need to reference (e.g., build artifacts, logs, `node_modules`). Reducing the total number of files crawled is the most effective way to improve performance.
-
-2.  **Disable Fuzzy Search:** If ignoring files is not enough, you can disable fuzzy search by setting `disableFuzzySearch` to `true` in your `settings.json` file. This will use a simpler, non-fuzzy matching algorithm, which can be faster.
-
-3.  **Disable Recursive File Search:** As a last resort, you can disable recursive file search entirely by setting `enableRecursiveFileSearch` to `false`. This will be the fastest option as it avoids a recursive crawl of your project. However, it means you will need to type the full path to files when using `@` completions.
-
-- **`coreTools`** (array of strings):
-  - **Description:** Allows you to specify a list of core tool names that should be made available to the model. This can be used to restrict the set of built-in tools. See [Built-in Tools](../core/tools-api.md#built-in-tools) for a list of core tools. You can also specify command-specific restrictions for tools that support it, like the `ShellTool`. For example, `"coreTools": ["ShellTool(ls -l)"]` will only allow the `ls -l` command to be executed.
-  - **Default:** All tools available for use by the Gemini model.
-  - **Example:** `"coreTools": ["ReadFileTool", "GlobTool", "ShellTool(ls)"]`.
-
-- **`allowedTools`** (array of strings):
+- **`general.preferredEditor`** (string):
+  - **Description:** The preferred editor to open files in.
   - **Default:** `undefined`
-  - **Description:** A list of tool names that will bypass the confirmation dialog. This is useful for tools that you trust and use frequently. The match semantics are the same as `coreTools`.
-  - **Example:** `"allowedTools": ["ShellTool(git status)"]`.
 
-- **`excludeTools`** (array of strings):
-  - **Description:** Allows you to specify a list of core tool names that should be excluded from the model. A tool listed in both `excludeTools` and `coreTools` is excluded. You can also specify command-specific restrictions for tools that support it, like the `ShellTool`. For example, `"excludeTools": ["ShellTool(rm -rf)"]` will block the `rm -rf` command.
-  - **Default**: No tools excluded.
-  - **Example:** `"excludeTools": ["run_shell_command", "findFiles"]`.
-  - **Security Note:** Command-specific restrictions in
-    `excludeTools` for `run_shell_command` are based on simple string matching and can be easily bypassed. This feature is **not a security mechanism** and should not be relied upon to safely execute untrusted code. It is recommended to use `coreTools` to explicitly select commands
-    that can be executed.
-
-- **`allowMCPServers`** (array of strings):
-  - **Description:** Allows you to specify a list of MCP server names that should be made available to the model. This can be used to restrict the set of MCP servers to connect to. Note that this will be ignored if `--allowed-mcp-server-names` is set.
-  - **Default:** All MCP servers are available for use by the Gemini model.
-  - **Example:** `"allowMCPServers": ["myPythonServer"]`.
-  - **Security Note:** This uses simple string matching on MCP server names, which can be modified. If you're a system administrator looking to prevent users from bypassing this, consider configuring the `mcpServers` at the system settings level such that the user will not be able to configure any MCP servers of their own. This should not be used as an airtight security mechanism.
-
-- **`excludeMCPServers`** (array of strings):
-  - **Description:** Allows you to specify a list of MCP server names that should be excluded from the model. A server listed in both `excludeMCPServers` and `allowMCPServers` is excluded. Note that this will be ignored if `--allowed-mcp-server-names` is set.
-  - **Default**: No MCP servers excluded.
-  - **Example:** `"excludeMCPServers": ["myNodeServer"]`.
-  - **Security Note:** This uses simple string matching on MCP server names, which can be modified. If you're a system administrator looking to prevent users from bypassing this, consider configuring the `mcpServers` at the system settings level such that the user will not be able to configure any MCP servers of their own. This should not be used as an airtight security mechanism.
-
-- **`autoAccept`** (boolean):
-  - **Description:** Controls whether the CLI automatically accepts and executes tool calls that are considered safe (e.g., read-only operations) without explicit user confirmation. If set to `true`, the CLI will bypass the confirmation prompt for tools deemed safe.
+- **`general.vimMode`** (boolean):
+  - **Description:** Enable Vim keybindings.
   - **Default:** `false`
-  - **Example:** `"autoAccept": true`
 
-- **`theme`** (string):
-  - **Description:** Sets the visual [theme](./themes.md) for Gemini CLI.
-  - **Default:** `"Default"`
-  - **Example:** `"theme": "GitHub"`
-
-- **`vimMode`** (boolean):
-  - **Description:** Enables or disables vim mode for input editing. When enabled, the input area supports vim-style navigation and editing commands with NORMAL and INSERT modes. The vim mode status is displayed in the footer and persists between sessions.
+- **`general.disableAutoUpdate`** (boolean):
+  - **Description:** Disable automatic updates.
   - **Default:** `false`
-  - **Example:** `"vimMode": true`
 
-- **`sandbox`** (boolean or string):
-  - **Description:** Controls whether and how to use sandboxing for tool execution. If set to `true`, Gemini CLI uses a pre-built `gemini-cli-sandbox` Docker image. For more information, see [Sandboxing](#sandboxing).
+- **`general.disableUpdateNag`** (boolean):
+  - **Description:** Disable update notification prompts.
   - **Default:** `false`
-  - **Example:** `"sandbox": "docker"`
 
-- **`toolDiscoveryCommand`** (string):
-  - **Description:** Defines a custom shell command for discovering tools from your project. The shell command must return on `stdout` a JSON array of [function declarations](https://ai.google.dev/gemini-api/docs/function-calling#function-declarations). Tool wrappers are optional.
-  - **Default:** Empty
-  - **Example:** `"toolDiscoveryCommand": "bin/get_tools"`
+- **`general.checkpointing.enabled`** (boolean):
+  - **Description:** Enable session checkpointing for recovery.
+  - **Default:** `false`
 
-- **`toolCallCommand`** (string):
-  - **Description:** Defines a custom shell command for calling a specific tool that was discovered using `toolDiscoveryCommand`. The shell command must meet the following criteria:
+#### `ui`
+
+- **`ui.theme`** (string):
+  - **Description:** The color theme for the UI. See [Themes](./themes.md) for available options.
+  - **Default:** `undefined`
+
+- **`ui.customThemes`** (object):
+  - **Description:** Custom theme definitions.
+  - **Default:** `{}`
+
+- **`ui.hideWindowTitle`** (boolean):
+  - **Description:** Hide the window title bar.
+  - **Default:** `false`
+
+- **`ui.hideTips`** (boolean):
+  - **Description:** Hide helpful tips in the UI.
+  - **Default:** `false`
+
+- **`ui.hideBanner`** (boolean):
+  - **Description:** Hide the application banner.
+  - **Default:** `false`
+
+- **`ui.hideFooter`** (boolean):
+  - **Description:** Hide the footer from the UI.
+  - **Default:** `false`
+
+- **`ui.showMemoryUsage`** (boolean):
+  - **Description:** Display memory usage information in the UI.
+  - **Default:** `false`
+
+- **`ui.showLineNumbers`** (boolean):
+  - **Description:** Show line numbers in the chat.
+  - **Default:** `false`
+
+- **`ui.showCitations`** (boolean):
+  - **Description:** Show citations for generated text in the chat.
+  - **Default:** `false`
+
+- **`ui.accessibility.disableLoadingPhrases`** (boolean):
+  - **Description:** Disable loading phrases for accessibility.
+  - **Default:** `false`
+
+#### `ide`
+
+- **`ide.enabled`** (boolean):
+  - **Description:** Enable IDE integration mode.
+  - **Default:** `false`
+
+- **`ide.hasSeenNudge`** (boolean):
+  - **Description:** Whether the user has seen the IDE integration nudge.
+  - **Default:** `false`
+
+#### `privacy`
+
+- **`privacy.usageStatisticsEnabled`** (boolean):
+  - **Description:** Enable collection of usage statistics.
+  - **Default:** `true`
+
+#### `model`
+
+- **`model.name`** (string):
+  - **Description:** The Gemini model to use for conversations.
+  - **Default:** `undefined`
+
+- **`model.maxSessionTurns`** (number):
+  - **Description:** Maximum number of user/model/tool turns to keep in a session. -1 means unlimited.
+  - **Default:** `-1`
+
+- **`model.summarizeToolOutput`** (object):
+  - **Description:** Enables or disables the summarization of tool output. You can specify the token budget for the summarization using the `tokenBudget` setting. Note: Currently only the `run_shell_command` tool is supported. For example `{"run_shell_command": {"tokenBudget": 2000}}`
+  - **Default:** `undefined`
+
+- **`model.chatCompression.contextPercentageThreshold`** (number):
+  - **Description:** Sets the threshold for chat history compression as a percentage of the model's total token limit. This is a value between 0 and 1 that applies to both automatic compression and the manual `/compress` command. For example, a value of `0.6` will trigger compression when the chat history exceeds 60% of the token limit.
+  - **Default:** `0.7`
+
+- **`model.skipNextSpeakerCheck`** (boolean):
+  - **Description:** Skip the next speaker check.
+  - **Default:** `false`
+
+#### `context`
+
+- **`context.fileName`** (string or array of strings):
+  - **Description:** The name of the context file(s).
+  - **Default:** `undefined`
+
+- **`context.importFormat`** (string):
+  - **Description:** The format to use when importing memory.
+  - **Default:** `undefined`
+
+- **`context.discoveryMaxDirs`** (number):
+  - **Description:** Maximum number of directories to search for memory.
+  - **Default:** `200`
+
+- **`context.includeDirectories`** (array):
+  - **Description:** Additional directories to include in the workspace context. Missing directories will be skipped with a warning.
+  - **Default:** `[]`
+
+- **`context.loadFromIncludeDirectories`** (boolean):
+  - **Description:** Controls the behavior of the `/memory refresh` command. If set to `true`, `GEMINI.md` files should be loaded from all directories that are added. If set to `false`, `GEMINI.md` should only be loaded from the current directory.
+  - **Default:** `false`
+
+- **`context.fileFiltering.respectGitIgnore`** (boolean):
+  - **Description:** Respect .gitignore files when searching.
+  - **Default:** `true`
+
+- **`context.fileFiltering.respectGeminiIgnore`** (boolean):
+  - **Description:** Respect .geminiignore files when searching.
+  - **Default:** `true`
+
+- **`context.fileFiltering.enableRecursiveFileSearch`** (boolean):
+  - **Description:** Whether to enable searching recursively for filenames under the current tree when completing `@` prefixes in the prompt.
+  - **Default:** `true`
+
+#### `tools`
+
+- **`tools.sandbox`** (boolean or string):
+  - **Description:** Sandbox execution environment (can be a boolean or a path string).
+  - **Default:** `undefined`
+
+- **`tools.usePty`** (boolean):
+  - **Description:** Use node-pty for shell command execution. Fallback to child_process still applies.
+  - **Default:** `false`
+
+- **`tools.core`** (array of strings):
+  - **Description:** This can be used to restrict the set of built-in tools [with an allowlist](./enterprise.md#restricting-tool-access). See [Built-in Tools](../core/tools-api.md#built-in-tools) for a list of core tools. The match semantics are the same as `tools.allowed`.
+  - **Default:** `undefined`
+
+- **`tools.exclude`** (array of strings):
+  - **Description:** Tool names to exclude from discovery.
+  - **Default:** `undefined`
+
+- **`tools.allowed`** (array of strings):
+  - **Description:** A list of tool names that will bypass the confirmation dialog. This is useful for tools that you trust and use frequently. For example, `["run_shell_command(git)", "run_shell_command(npm test)"]` will skip the confirmation dialog to run any `git` and `npm test` commands. See [Shell Tool command restrictions](../tools/shell.md#command-restrictions) for details on prefix matching, command chaining, etc.
+  - **Default:** `undefined`
+
+- **`tools.discoveryCommand`** (string):
+  - **Description:** Command to run for tool discovery.
+  - **Default:** `undefined`
+
+- **`tools.callCommand`** (string):
+  - **Description:** Defines a custom shell command for calling a specific tool that was discovered using `tools.discoveryCommand`. The shell command must meet the following criteria:
     - It must take function `name` (exactly as in [function declaration](https://ai.google.dev/gemini-api/docs/function-calling#function-declarations)) as first command line argument.
     - It must read function arguments as JSON on `stdin`, analogous to [`functionCall.args`](https://cloud.google.com/vertex-ai/generative-ai/docs/model-reference/inference#functioncall).
     - It must return function output as JSON on `stdout`, analogous to [`functionResponse.response.content`](https://cloud.google.com/vertex-ai/generative-ai/docs/model-reference/inference#functionresponse).
-  - **Default:** Empty
-  - **Example:** `"toolCallCommand": "bin/call_tool"`
+  - **Default:** `undefined`
 
-- **`mcpServers`** (object):
-  - **Description:** Configures connections to one or more Model-Context Protocol (MCP) servers for discovering and using custom tools. Gemini CLI attempts to connect to each configured MCP server to discover available tools. If multiple MCP servers expose a tool with the same name, the tool names will be prefixed with the server alias you defined in the configuration (e.g., `serverAlias__actualToolName`) to avoid conflicts. Note that the system might strip certain schema properties from MCP tool definitions for compatibility. At least one of `command`, `url`, or `httpUrl` must be provided. If multiple are specified, the order of precedence is `httpUrl`, then `url`, then `command`.
-  - **Default:** Empty
-  - **Properties:**
-    - **`<SERVER_NAME>`** (object): The server parameters for the named server.
-      - `command` (string, optional): The command to execute to start the MCP server via standard I/O.
-      - `args` (array of strings, optional): Arguments to pass to the command.
-      - `env` (object, optional): Environment variables to set for the server process.
-      - `cwd` (string, optional): The working directory in which to start the server.
-      - `url` (string, optional): The URL of an MCP server that uses Server-Sent Events (SSE) for communication.
-      - `httpUrl` (string, optional): The URL of an MCP server that uses streamable HTTP for communication.
-      - `headers` (object, optional): A map of HTTP headers to send with requests to `url` or `httpUrl`.
-      - `timeout` (number, optional): Timeout in milliseconds for requests to this MCP server.
-      - `trust` (boolean, optional): Trust this server and bypass all tool call confirmations.
-      - `description` (string, optional): A brief description of the server, which may be used for display purposes.
-      - `includeTools` (array of strings, optional): List of tool names to include from this MCP server. When specified, only the tools listed here will be available from this server (whitelist behavior). If not specified, all tools from the server are enabled by default.
-      - `excludeTools` (array of strings, optional): List of tool names to exclude from this MCP server. Tools listed here will not be available to the model, even if they are exposed by the server. **Note:** `excludeTools` takes precedence over `includeTools` - if a tool is in both lists, it will be excluded.
-  - **Example:**
-    ```json
-    "mcpServers": {
-      "myPythonServer": {
-        "command": "python",
-        "args": ["mcp_server.py", "--port", "8080"],
-        "cwd": "./mcp_tools/python",
-        "timeout": 5000,
-        "includeTools": ["safe_tool", "file_reader"],
-      },
-      "myNodeServer": {
-        "command": "node",
-        "args": ["mcp_server.js"],
-        "cwd": "./mcp_tools/node",
-        "excludeTools": ["dangerous_tool", "file_deleter"]
-      },
-      "myDockerServer": {
-        "command": "docker",
-        "args": ["run", "-i", "--rm", "-e", "API_KEY", "ghcr.io/foo/bar"],
-        "env": {
-          "API_KEY": "$MY_API_TOKEN"
-        }
-      },
-      "mySseServer": {
-        "url": "http://localhost:8081/events",
-        "headers": {
-          "Authorization": "Bearer $MY_SSE_TOKEN"
-        },
-        "description": "An example SSE-based MCP server."
-      },
-      "myStreamableHttpServer": {
-        "httpUrl": "http://localhost:8082/stream",
-        "headers": {
-          "X-API-Key": "$MY_HTTP_API_KEY"
-        },
-        "description": "An example Streamable HTTP-based MCP server."
-      }
-    }
-    ```
+#### `mcp`
 
-- **`checkpointing`** (object):
-  - **Description:** Configures the checkpointing feature, which allows you to save and restore conversation and file states. See the [Checkpointing documentation](../checkpointing.md) for more details.
-  - **Default:** `{"enabled": false}`
-  - **Properties:**
-    - **`enabled`** (boolean): When `true`, the `/restore` command is available.
+- **`mcp.serverCommand`** (string):
+  - **Description:** Command to start an MCP server.
+  - **Default:** `undefined`
 
-- **`preferredEditor`** (string):
-  - **Description:** Specifies the preferred editor to use for viewing diffs.
-  - **Default:** `vscode`
-  - **Example:** `"preferredEditor": "vscode"`
+- **`mcp.allowed`** (array of strings):
+  - **Description:** An allowlist of MCP servers to allow.
+  - **Default:** `undefined`
 
-- **`telemetry`** (object)
-  - **Description:** Configures logging and metrics collection for Gemini CLI. For more information, see [Telemetry](../telemetry.md).
-  - **Default:** `{"enabled": false, "target": "local", "otlpEndpoint": "http://localhost:4317", "logPrompts": true}`
-  - **Properties:**
-    - **`enabled`** (boolean): Whether or not telemetry is enabled.
-    - **`target`** (string): The destination for collected telemetry. Supported values are `local` and `gcp`.
-    - **`otlpEndpoint`** (string): The endpoint for the OTLP Exporter.
-    - **`logPrompts`** (boolean): Whether or not to include the content of user prompts in the logs.
-  - **Example:**
-    ```json
-    "telemetry": {
-      "enabled": true,
-      "target": "local",
-      "otlpEndpoint": "http://localhost:16686",
-      "logPrompts": false
-    }
-    ```
-- **`usageStatisticsEnabled`** (boolean):
-  - **Description:** Enables or disables the collection of usage statistics. See [Usage Statistics](#usage-statistics) for more information.
-  - **Default:** `true`
-  - **Example:**
-    ```json
-    "usageStatisticsEnabled": false
-    ```
+- **`mcp.excluded`** (array of strings):
+  - **Description:** A denylist of MCP servers to exclude.
+  - **Default:** `undefined`
 
-- **`hideTips`** (boolean):
-  - **Description:** Enables or disables helpful tips in the CLI interface.
+#### `security`
+
+- **`security.folderTrust.enabled`** (boolean):
+  - **Description:** Setting to track whether Folder trust is enabled.
   - **Default:** `false`
-  - **Example:**
 
-    ```json
-    "hideTips": true
-    ```
+- **`security.auth.selectedType`** (string):
+  - **Description:** The currently selected authentication type.
+  - **Default:** `undefined`
 
-- **`hideBanner`** (boolean):
-  - **Description:** Enables or disables the startup banner (ASCII art logo) in the CLI interface.
+- **`security.auth.enforcedType`** (string):
+  - **Description:** The required auth type (useful for enterprises).
+  - **Default:** `undefined`
+
+- **`security.auth.useExternal`** (boolean):
+  - **Description:** Whether to use an external authentication flow.
+  - **Default:** `undefined`
+
+#### `advanced`
+
+- **`advanced.autoConfigureMemory`** (boolean):
+  - **Description:** Automatically configure Node.js memory limits.
   - **Default:** `false`
-  - **Example:**
 
-    ```json
-    "hideBanner": true
-    ```
+- **`advanced.dnsResolutionOrder`** (string):
+  - **Description:** The DNS resolution order.
+  - **Default:** `undefined`
 
-- **`maxSessionTurns`** (number):
-  - **Description:** Sets the maximum number of turns for a session. If the session exceeds this limit, the CLI will stop processing and start a new chat.
-  - **Default:** `-1` (unlimited)
-  - **Example:**
-    ```json
-    "maxSessionTurns": 10
-    ```
+- **`advanced.excludedEnvVars`** (array of strings):
+  - **Description:** Environment variables to exclude from project context.
+  - **Default:** `["DEBUG","DEBUG_MODE"]`
 
-- **`summarizeToolOutput`** (object):
-  - **Description:** Enables or disables the summarization of tool output. You can specify the token budget for the summarization using the `tokenBudget` setting.
-  - Note: Currently only the `run_shell_command` tool is supported.
-  - **Default:** `{}` (Disabled by default)
-  - **Example:**
-    ```json
-    "summarizeToolOutput": {
-      "run_shell_command": {
-        "tokenBudget": 2000
-      }
-    }
-    ```
+- **`advanced.bugCommand`** (object):
+  - **Description:** Configuration for the bug report command.
+  - **Default:** `undefined`
 
-- **`excludedProjectEnvVars`** (array of strings):
-  - **Description:** Specifies environment variables that should be excluded from being loaded from project `.env` files. This prevents project-specific environment variables (like `DEBUG=true`) from interfering with gemini-cli behavior. Variables from `.gemini/.env` files are never excluded.
-  - **Default:** `["DEBUG", "DEBUG_MODE"]`
-  - **Example:**
-    ```json
-    "excludedProjectEnvVars": ["DEBUG", "DEBUG_MODE", "NODE_ENV"]
-    ```
+#### `mcpServers`
 
-- **`includeDirectories`** (array of strings):
-  - **Description:** Specifies an array of additional absolute or relative paths to include in the workspace context. Missing directories will be skipped with a warning by default. Paths can use `~` to refer to the user's home directory. This setting can be combined with the `--include-directories` command-line flag.
-  - **Default:** `[]`
-  - **Example:**
-    ```json
-    "includeDirectories": [
-      "/path/to/another/project",
-      "../shared-library",
-      "~/common-utils"
-    ]
-    ```
+Configures connections to one or more Model-Context Protocol (MCP) servers for discovering and using custom tools. Gemini CLI attempts to connect to each configured MCP server to discover available tools. If multiple MCP servers expose a tool with the same name, the tool names will be prefixed with the server alias you defined in the configuration (e.g., `serverAlias__actualToolName`) to avoid conflicts. Note that the system might strip certain schema properties from MCP tool definitions for compatibility. At least one of `command`, `url`, or `httpUrl` must be provided. If multiple are specified, the order of precedence is `httpUrl`, then `url`, then `command`.
 
-- **`loadMemoryFromIncludeDirectories`** (boolean):
-  - **Description:** Controls the behavior of the `/memory refresh` command. If set to `true`, `GEMINI.md` files should be loaded from all directories that are added. If set to `false`, `GEMINI.md` should only be loaded from the current directory.
-  - **Default:** `false`
-  - **Example:**
-    ```json
-    "loadMemoryFromIncludeDirectories": true
-    ```
+- **`mcpServers.<SERVER_NAME>`** (object): The server parameters for the named server.
+  - `command` (string, optional): The command to execute to start the MCP server via standard I/O.
+  - `args` (array of strings, optional): Arguments to pass to the command.
+  - `env` (object, optional): Environment variables to set for the server process.
+  - `cwd` (string, optional): The working directory in which to start the server.
+  - `url` (string, optional): The URL of an MCP server that uses Server-Sent Events (SSE) for communication.
+  - `httpUrl` (string, optional): The URL of an MCP server that uses streamable HTTP for communication.
+  - `headers` (object, optional): A map of HTTP headers to send with requests to `url` or `httpUrl`.
+  - `timeout` (number, optional): Timeout in milliseconds for requests to this MCP server.
+  - `trust` (boolean, optional): Trust this server and bypass all tool call confirmations.
+  - `description` (string, optional): A brief description of the server, which may be used for display purposes.
+  - `includeTools` (array of strings, optional): List of tool names to include from this MCP server. When specified, only the tools listed here will be available from this server (allowlist behavior). If not specified, all tools from the server are enabled by default.
+  - `excludeTools` (array of strings, optional): List of tool names to exclude from this MCP server. Tools listed here will not be available to the model, even if they are exposed by the server. **Note:** `excludeTools` takes precedence over `includeTools` - if a tool is in both lists, it will be excluded.
 
-- **`chatCompression`** (object):
-  - **Description:** Controls the settings for chat history compression, both automatic and
-    when manually invoked through the /compress command.
-  - **Properties:**
-    - **`contextPercentageThreshold`** (number): A value between 0 and 1 that specifies the token threshold for compression as a percentage of the model's total token limit. For example, a value of `0.6` will trigger compression when the chat history exceeds 60% of the token limit.
-  - **Example:**
-    ```json
-    "chatCompression": {
-      "contextPercentageThreshold": 0.6
-    }
-    ```
+#### `telemetry`
 
-- **`showLineNumbers`** (boolean):
-  - **Description:** Controls whether line numbers are displayed in code blocks in the CLI output.
-  - **Default:** `true`
-  - **Example:**
-    ```json
-    "showLineNumbers": false
-    ```
+Configures logging and metrics collection for Gemini CLI. For more information, see [Telemetry](../telemetry.md).
 
-- **`accessibility`** (object):
-  - **Description:** Configures accessibility features for the CLI.
-  - **Properties:**
-    - **`screenReader`** (boolean): Enables screen reader mode, which adjusts the TUI for better compatibility with screen readers. This can also be enabled with the `--screen-reader` command-line flag, which will take precedence over the setting.
-    - **`disableLoadingPhrases`** (boolean): Disables the display of loading phrases during operations.
-  - **Default:** `{"screenReader": false, "disableLoadingPhrases": false}`
-  - **Example:**
-    ```json
-    "accessibility": {
-      "screenReader": true,
-      "disableLoadingPhrases": true
-    }
-    ```
+- **Properties:**
+  - **`enabled`** (boolean): Whether or not telemetry is enabled.
+  - **`target`** (string): The destination for collected telemetry. Supported values are `local` and `gcp`.
+  - **`otlpEndpoint`** (string): The endpoint for the OTLP Exporter.
+  - **`otlpProtocol`** (string): The protocol for the OTLP Exporter (`grpc` or `http`).
+  - **`logPrompts`** (boolean): Whether or not to include the content of user prompts in the logs.
+  - **`outfile`** (string): The file to write telemetry to when `target` is `local`.
 
-### Example `settings.json`:
+### Example `settings.json`
+
+Here is an example of a `settings.json` file with the nested structure, new as of v0.3.0:
 
 ```json
 {
-  "theme": "GitHub",
-  "sandbox": "docker",
-  "toolDiscoveryCommand": "bin/get_tools",
-  "toolCallCommand": "bin/call_tool",
+  "general": {
+    "vimMode": true,
+    "preferredEditor": "code"
+  },
+  "ui": {
+    "theme": "GitHub",
+    "hideBanner": true,
+    "hideTips": false
+  },
+  "tools": {
+    "sandbox": "docker",
+    "discoveryCommand": "bin/get_tools",
+    "callCommand": "bin/call_tool",
+    "exclude": ["write_file"]
+  },
   "mcpServers": {
     "mainServer": {
       "command": "bin/mcp_server.py"
@@ -366,18 +339,29 @@ If you are experiencing performance issues with file searching (e.g., with `@` c
     "otlpEndpoint": "http://localhost:4317",
     "logPrompts": true
   },
-  "usageStatisticsEnabled": true,
-  "hideTips": false,
-  "hideBanner": false,
-  "maxSessionTurns": 10,
-  "summarizeToolOutput": {
-    "run_shell_command": {
-      "tokenBudget": 100
+  "privacy": {
+    "usageStatisticsEnabled": true
+  },
+  "model": {
+    "name": "gemini-1.5-pro-latest",
+    "maxSessionTurns": 10,
+    "summarizeToolOutput": {
+      "run_shell_command": {
+        "tokenBudget": 100
+      }
     }
   },
-  "excludedProjectEnvVars": ["DEBUG", "DEBUG_MODE", "NODE_ENV"],
-  "includeDirectories": ["path/to/dir1", "~/path/to/dir2", "../path/to/dir3"],
-  "loadMemoryFromIncludeDirectories": true
+  "context": {
+    "fileName": ["CONTEXT.md", "GEMINI.md"],
+    "includeDirectories": ["path/to/dir1", "~/path/to/dir2", "../path/to/dir3"],
+    "loadFromIncludeDirectories": true,
+    "fileFiltering": {
+      "respectGitIgnore": false
+    }
+  },
+  "advanced": {
+    "excludedEnvVars": ["DEBUG", "DEBUG_MODE", "NODE_ENV"]
+  }
 }
 ```
 
@@ -399,7 +383,7 @@ The CLI automatically loads environment variables from an `.env` file. The loadi
 2.  If not found, it searches upwards in parent directories until it finds an `.env` file or reaches the project root (identified by a `.git` folder) or the home directory.
 3.  If still not found, it looks for `~/.env` (in the user's home directory).
 
-**Environment Variable Exclusion:** Some environment variables (like `DEBUG` and `DEBUG_MODE`) are automatically excluded from being loaded from project `.env` files to prevent interference with gemini-cli behavior. Variables from `.gemini/.env` files are never excluded. You can customize this behavior using the `excludedProjectEnvVars` setting in your `settings.json` file.
+**Environment Variable Exclusion:** Some environment variables (like `DEBUG` and `DEBUG_MODE`) are automatically excluded from being loaded from project `.env` files to prevent interference with gemini-cli behavior. Variables from `.gemini/.env` files are never excluded. You can customize this behavior using the `advanced.excludedEnvVars` setting in your `settings.json` file.
 
 - **`GEMINI_API_KEY`**:
   - Your API key for the Gemini API.
@@ -514,13 +498,13 @@ Arguments passed directly when running the CLI can override other configurations
   - 5 directories can be added at maximum.
   - Example: `--include-directories /path/to/project1,/path/to/project2` or `--include-directories /path/to/project1 --include-directories /path/to/project2`
 - **`--screen-reader`**:
-  - Enables screen reader mode for accessibility.
+  - Enables screen reader mode, which adjusts the TUI for better compatibility with screen readers.
 - **`--version`**:
   - Displays the version of the CLI.
 
 ## Context Files (Hierarchical Instructional Context)
 
-While not strictly configuration for the CLI's _behavior_, context files (defaulting to `GEMINI.md` but configurable via the `contextFileName` setting) are crucial for configuring the _instructional context_ (also referred to as "memory") provided to the Gemini model. This powerful feature allows you to give project-specific instructions, coding style guides, or any relevant background information to the AI, making its responses more tailored and accurate to your needs. The CLI includes UI elements, such as an indicator in the footer showing the number of loaded context files, to keep you informed about the active context.
+While not strictly configuration for the CLI's _behavior_, context files (defaulting to `GEMINI.md` but configurable via the `context.fileName` setting) are crucial for configuring the _instructional context_ (also referred to as "memory") provided to the Gemini model. This powerful feature allows you to give project-specific instructions, coding style guides, or any relevant background information to the AI, making its responses more tailored and accurate to your needs. The CLI includes UI elements, such as an indicator in the footer showing the number of loaded context files, to keep you informed about the active context.
 
 - **Purpose:** These Markdown files contain instructions, guidelines, or context that you want the Gemini model to be aware of during your interactions. The system is designed to manage this instructional context hierarchically.
 
@@ -561,13 +545,13 @@ This example demonstrates how you can provide general project context, specific
 
 - **Hierarchical Loading and Precedence:** The CLI implements a sophisticated hierarchical memory system by loading context files (e.g., `GEMINI.md`) from several locations. Content from files lower in this list (more specific) typically overrides or supplements content from files higher up (more general). The exact concatenation order and final context can be inspected using the `/memory show` command. The typical loading order is:
   1.  **Global Context File:**
-      - Location: `~/.gemini/<contextFileName>` (e.g., `~/.gemini/GEMINI.md` in your user home directory).
+      - Location: `~/.gemini/<configured-context-filename>` (e.g., `~/.gemini/GEMINI.md` in your user home directory).
       - Scope: Provides default instructions for all your projects.
   2.  **Project Root & Ancestors Context Files:**
       - Location: The CLI searches for the configured context file in the current working directory and then in each parent directory up to either the project root (identified by a `.git` folder) or your home directory.
       - Scope: Provides context relevant to the entire project or a significant portion of it.
   3.  **Sub-directory Context Files (Contextual/Local):**
-      - Location: The CLI also scans for the configured context file in subdirectories _below_ the current working directory (respecting common ignore patterns like `node_modules`, `.git`, etc.). The breadth of this search is limited to 200 directories by default, but can be configured with a `memoryDiscoveryMaxDirs` field in your `settings.json` file.
+      - Location: The CLI also scans for the configured context file in subdirectories _below_ the current working directory (respecting common ignore patterns like `node_modules`, `.git`, etc.). The breadth of this search is limited to 200 directories by default, but can be configured with the `context.discoveryMaxDirs` setting in your `settings.json` file.
       - Scope: Allows for highly specific instructions relevant to a particular component, module, or subsection of your project.
 - **Concatenation & UI Indication:** The contents of all found context files are concatenated (with separators indicating their origin and path) and provided as part of the system prompt to the Gemini model. The CLI footer displays the count of loaded context files, giving you a quick visual cue about the active instructional context.
 - **Importing Content:** You can modularize your context files by importing other Markdown files using the `@path/to/file.md` syntax. For more details, see the [Memory Import Processor documentation](../core/memport.md).
@@ -625,10 +609,12 @@ To help us improve the Gemini CLI, we collect anonymized usage statistics. This
 
 **How to opt out:**
 
-You can opt out of usage statistics collection at any time by setting the `usageStatisticsEnabled` property to `false` in your `settings.json` file:
+You can opt out of usage statistics collection at any time by setting the `usageStatisticsEnabled` property to `false` under the `privacy` category in your `settings.json` file:
 
 ```json
 {
-  "usageStatisticsEnabled": false
+  "privacy": {
+    "usageStatisticsEnabled": false
+  }
 }
 ```

docs/cli/enterprise.md

@@ -25,8 +25,12 @@ Here is how settings from different levels are combined.
 
   ```json
   {
-    "theme": "default-corporate-theme",
-    "includeDirectories": ["/etc/gemini-cli/common-context"]
+    "ui": {
+      "theme": "default-corporate-theme"
+    },
+    "context": {
+      "includeDirectories": ["/etc/gemini-cli/common-context"]
+    }
   }
   ```
 
@@ -34,7 +38,9 @@ Here is how settings from different levels are combined.
 
   ```json
   {
-    "theme": "user-preferred-dark-theme",
+    "ui": {
+      "theme": "user-preferred-dark-theme"
+    },
     "mcpServers": {
       "corp-server": {
         "command": "/usr/local/bin/corp-server-dev"
@@ -43,7 +49,9 @@ Here is how settings from different levels are combined.
         "command": "npm start --prefix ~/tools/my-tool"
       }
     },
-    "includeDirectories": ["~/gemini-context"]
+    "context": {
+      "includeDirectories": ["~/gemini-context"]
+    }
   }
   ```
 
@@ -51,26 +59,34 @@ Here is how settings from different levels are combined.
 
   ```json
   {
-    "theme": "project-specific-light-theme",
+    "ui": {
+      "theme": "project-specific-light-theme"
+    },
     "mcpServers": {
       "project-tool": {
         "command": "npm start"
       }
     },
-    "includeDirectories": ["./project-context"]
+    "context": {
+      "includeDirectories": ["./project-context"]
+    }
   }
   ```
 
 - **System Overrides `settings.json`:**
   ```json
   {
-    "theme": "system-enforced-theme",
+    "ui": {
+      "theme": "system-enforced-theme"
+    },
     "mcpServers": {
       "corp-server": {
         "command": "/usr/local/bin/corp-server-prod"
       }
     },
-    "includeDirectories": ["/etc/gemini-cli/global-context"]
+    "context": {
+      "includeDirectories": ["/etc/gemini-cli/global-context"]
+    }
   }
   ```
 
@@ -79,7 +95,9 @@ This results in the following merged configuration:
 - **Final Merged Configuration:**
   ```json
   {
-    "theme": "system-enforced-theme",
+    "ui": {
+      "theme": "system-enforced-theme"
+    },
     "mcpServers": {
       "corp-server": {
         "command": "/usr/local/bin/corp-server-prod"
@@ -91,12 +109,14 @@ This results in the following merged configuration:
         "command": "npm start"
       }
     },
-    "includeDirectories": [
-      "/etc/gemini-cli/common-context",
-      "~/gemini-context",
-      "./project-context",
-      "/etc/gemini-cli/global-context"
-    ]
+    "context": {
+      "includeDirectories": [
+        "/etc/gemini-cli/common-context",
+        "~/gemini-context",
+        "./project-context",
+        "/etc/gemini-cli/global-context"
+      ]
+    }
   }
   ```
 
@@ -117,7 +137,7 @@ By using the system settings file, you can enforce the security and configuratio
 
 ## Restricting Tool Access
 
-You can significantly enhance security by controlling which tools the Gemini model can use. This is achieved through the `coreTools` and `excludeTools` settings. For a list of available tools, see the [Tools documentation](../tools/index.md).
+You can significantly enhance security by controlling which tools the Gemini model can use. This is achieved through the `tools.core` and `tools.exclude` settings. For a list of available tools, see the [Tools documentation](../tools/index.md).
 
 ### Allowlisting with `coreTools`
 
@@ -127,7 +147,9 @@ The most secure approach is to explicitly add the tools and commands that users
 
 ```json
 {
-  "coreTools": ["ReadFileTool", "GlobTool", "ShellTool(ls)"]
+  "tools": {
+    "core": ["ReadFileTool", "GlobTool", "ShellTool(ls)"]
+  }
 }
 ```
 
@@ -139,7 +161,9 @@ Alternatively, you can add specific tools that are considered dangerous in your
 
 ```json
 {
-  "excludeTools": ["ShellTool(rm -rf)"]
+  "tools": {
+    "exclude": ["ShellTool(rm -rf)"]
+  }
 }
 ```
 
@@ -172,7 +196,9 @@ Following the principle of least privilege, it is highly recommended to use `inc
 
 ```json
 {
-  "allowMCPServers": ["third-party-analyzer"],
+  "mcp": {
+    "allowed": ["third-party-analyzer"]
+  },
   "mcpServers": {
     "third-party-analyzer": {
       "command": "/usr/local/bin/start-3p-analyzer.sh",
@@ -187,7 +213,7 @@ Following the principle of least privilege, it is highly recommended to use `inc
 To create a secure, centrally-managed catalog of tools, the system administrator **must** do both of the following in the system-level `settings.json` file:
 
 1.  **Define the full configuration** for every approved server in the `mcpServers` object. This ensures that even if a user defines a server with the same name, the secure system-level definition will take precedence.
-2.  **Add the names** of those servers to an allowlist using the `allowMCPServers` setting. This is a critical security step that prevents users from running any servers that are not on this list. If this setting is omitted, the CLI will merge and allow any server defined by the user.
+2.  **Add the names** of those servers to an allowlist using the `mcp.allowed` setting. This is a critical security step that prevents users from running any servers that are not on this list. If this setting is omitted, the CLI will merge and allow any server defined by the user.
 
 **Example System `settings.json`:**
 
@@ -198,7 +224,9 @@ To create a secure, centrally-managed catalog of tools, the system administrator
 
 ```json
 {
-  "allowMCPServers": ["corp-data-api", "source-code-analyzer"],
+  "mcp": {
+    "allowed": ["corp-data-api", "source-code-analyzer"]
+  },
   "mcpServers": {
     "corp-data-api": {
       "command": "/usr/local/bin/start-corp-api.sh",
@@ -211,16 +239,16 @@ To create a secure, centrally-managed catalog of tools, the system administrator
 }
 ```
 
-This pattern is more secure because it uses both definition and an allowlist. Any server a user defines will either be overridden by the system definition (if it has the same name) or blocked because its name is not in the `allowMCPServers` list.
+This pattern is more secure because it uses both definition and an allowlist. Any server a user defines will either be overridden by the system definition (if it has the same name) or blocked because its name is not in the `mcp.allowed` list.
 
 ### Less Secure Pattern: Omitting the Allowlist
 
-If the administrator defines the `mcpServers` object but fails to also specify the `allowMCPServers` allowlist, users may add their own servers.
+If the administrator defines the `mcpServers` object but fails to also specify the `mcp.allowed` allowlist, users may add their own servers.
 
 **Example System `settings.json`:**
 
 This configuration defines servers but does not enforce the allowlist.
-The administrator has NOT included the "allowMCPServers" setting.
+The administrator has NOT included the "mcp.allowed" setting.
 
 ```json
 {
@@ -232,7 +260,7 @@ The administrator has NOT included the "allowMCPServers" setting.
 }
 ```
 
-In this scenario, a user can add their own server in their local `settings.json`. Because there is no `allowMCPServers` list to filter the merged results, the user's server will be added to the list of available tools and allowed to run.
+In this scenario, a user can add their own server in their local `settings.json`. Because there is no `mcp.allowed` list to filter the merged results, the user's server will be added to the list of available tools and allowed to run.
 
 ## Enforcing Sandboxing for Security
 
@@ -242,7 +270,9 @@ To mitigate the risk of potentially harmful operations, you can enforce the use
 
 ```json
 {
-  "sandbox": "docker"
+  "tools": {
+    "sandbox": "docker"
+  }
 }
 ```
 
@@ -287,42 +317,59 @@ For auditing and monitoring purposes, you can configure Gemini CLI to send telem
 
 **Note:** Ensure that `logPrompts` is set to `false` in an enterprise setting to avoid collecting potentially sensitive information from user prompts.
 
+## Authentication
+
+You can enforce a specific authentication method for all users by setting the `enforcedAuthType` in the system-level `settings.json` file. This prevents users from choosing a different authentication method. See the [Authentication docs](./authentication.md) for more details.
+
+**Example:** Enforce the use of Google login for all users.
+
+```json
+{
+  "enforcedAuthType": "oauth-personal"
+}
+```
+
+If a user has a different authentication method configured, they will be prompted to switch to the enforced method. In non-interactive mode, the CLI will exit with an error if the configured authentication method does not match the enforced one.
+
 ## Putting It All Together: Example System `settings.json`
 
 Here is an example of a system `settings.json` file that combines several of the patterns discussed above to create a secure, controlled environment for Gemini CLI.
 
 ```json
 {
-  "sandbox": "docker",
-
-  "coreTools": [
-    "ReadFileTool",
-    "GlobTool",
-    "ShellTool(ls)",
-    "ShellTool(cat)",
-    "ShellTool(grep)"
-  ],
-
+  "tools": {
+    "sandbox": "docker",
+    "core": [
+      "ReadFileTool",
+      "GlobTool",
+      "ShellTool(ls)",
+      "ShellTool(cat)",
+      "ShellTool(grep)"
+    ]
+  },
+  "mcp": {
+    "allowed": ["corp-tools"]
+  },
   "mcpServers": {
     "corp-tools": {
       "command": "/opt/gemini-tools/start.sh",
       "timeout": 5000
     }
   },
-  "allowMCPServers": ["corp-tools"],
-
   "telemetry": {
     "enabled": true,
     "target": "gcp",
     "otlpEndpoint": "https://telemetry-prod.example.com:4317",
     "logPrompts": false
   },
-
-  "bugCommand": {
-    "urlTemplate": "https://servicedesk.example.com/new-ticket?title={title}&details={info}"
+  "advanced": {
+    "bugCommand": {
+      "urlTemplate": "https://servicedesk.example.com/new-ticket?title={title}&details={info}"
+    }
   },
-
-  "usageStatisticsEnabled": false
+  "privacy": {
+    "usageStatisticsEnabled": false
+  }
 }
 ```
 

docs/cli/themes.md

@@ -46,25 +46,14 @@ Add a `customThemes` block to your user, project, or system `settings.json` file
 
 ```json
 {
-  "customThemes": {
-    "MyCustomTheme": {
-      "name": "MyCustomTheme",
-      "type": "custom",
-      "Background": "#181818",
-      "Foreground": "#F8F8F2",
-      "LightBlue": "#82AAFF",
-      "AccentBlue": "#61AFEF",
-      "AccentPurple": "#C678DD",
-      "AccentCyan": "#56B6C2",
-      "AccentGreen": "#98C379",
-      "AccentYellow": "#E5C07B",
-      "AccentRed": "#E06C75",
-      "Comment": "#5C6370",
-      "Gray": "#ABB2BF",
-      "DiffAdded": "#A6E3A1",
-      "DiffRemoved": "#F38BA8",
-      "DiffModified": "#89B4FA",
-      "GradientColors": ["#4796E4", "#847ACE", "#C3677F"]
+  "ui": {
+    "customThemes": {
+      "MyCustomTheme": {
+        "name": "MyCustomTheme",
+        "type": "custom",
+        "Background": "#181818",
+        ...
+      }
     }
   }
 }
@@ -115,7 +104,9 @@ To load a theme from a file, set the `theme` property in your `settings.json` to
 
 ```json
 {
-  "theme": "/path/to/your/theme.json"
+  "ui": {
+    "theme": "/path/to/your/theme.json"
+  }
 }
 ```
 
@@ -154,7 +145,7 @@ The theme file must be a valid JSON file that follows the same structure as a cu
 ### Using Your Custom Theme
 
 - Select your custom theme using the `/theme` command in Gemini CLI. Your custom theme will appear in the theme selection dialog.
-- Or, set it as the default by adding `"theme": "MyCustomTheme"` to your `settings.json`.
+- Or, set it as the default by adding `"theme": "MyCustomTheme"` to the `ui` object in your `settings.json`.
 - Custom themes can be set at the user, project, or system level, and follow the same [configuration precedence](./configuration.md) as other settings.
 
 ---

docs/core/tools-api.md

@@ -23,8 +23,8 @@ The Gemini CLI core (`packages/core`) features a robust system for defining, reg
 - **Tool Registry (`tool-registry.ts`):** A class (`ToolRegistry`) responsible for:
   - **Registering Tools:** Holding a collection of all available built-in tools (e.g., `ReadFileTool`, `ShellTool`).
   - **Discovering Tools:** It can also discover tools dynamically:
-    - **Command-based Discovery:** If `toolDiscoveryCommand` is configured in settings, this command is executed. It's expected to output JSON describing custom tools, which are then registered as `DiscoveredTool` instances.
-    - **MCP-based Discovery:** If `mcpServerCommand` is configured, the registry can connect to a Model Context Protocol (MCP) server to list and register tools (`DiscoveredMCPTool`).
+    - **Command-based Discovery:** If `tools.discoveryCommand` is configured in settings, this command is executed. It's expected to output JSON describing custom tools, which are then registered as `DiscoveredTool` instances.
+    - **MCP-based Discovery:** If `mcp.serverCommand` is configured, the registry can connect to a Model Context Protocol (MCP) server to list and register tools (`DiscoveredMCPTool`).
   - **Providing Schemas:** Exposing the `FunctionDeclaration` schemas of all registered tools to the Gemini model, so it knows what tools are available and how to use them.
   - **Retrieving Tools:** Allowing the core to get a specific tool by name for execution.
 
@@ -69,7 +69,7 @@ Each of these tools extends `BaseTool` and implements the required methods for i
 
 While direct programmatic registration of new tools by users isn't explicitly detailed as a primary workflow in the provided files for typical end-users, the architecture supports extension through:
 
-- **Command-based Discovery:** Advanced users or project administrators can define a `toolDiscoveryCommand` in `settings.json`. This command, when run by the Gemini CLI core, should output a JSON array of `FunctionDeclaration` objects. The core will then make these available as `DiscoveredTool` instances. The corresponding `toolCallCommand` would then be responsible for actually executing these custom tools.
+- **Command-based Discovery:** Advanced users or project administrators can define a `tools.discoveryCommand` in `settings.json`. This command, when run by the Gemini CLI core, should output a JSON array of `FunctionDeclaration` objects. The core will then make these available as `DiscoveredTool` instances. The corresponding `tools.callCommand` would then be responsible for actually executing these custom tools.
 - **MCP Server(s):** For more complex scenarios, one or more MCP servers can be set up and configured via the `mcpServers` setting in `settings.json`. The Gemini CLI core can then discover and use tools exposed by these servers. As mentioned, if you have multiple MCP servers, the tool names will be prefixed with the server name from your configuration (e.g., `serverAlias__actualToolName`).
 
 This tool system provides a flexible and powerful way to augment the Gemini model's capabilities, making the Gemini CLI a versatile assistant for a wide range of tasks.

docs/extension.md

@@ -1,19 +1,88 @@
 # Gemini CLI Extensions
 
-Gemini CLI supports extensions that can be used to configure and extend its functionality.
+_This documentation is up-to-date with the v0.4.0 release._
+
+Gemini CLI extensions package prompts, MCP servers, and custom commands into a familiar and user-friendly format. With extensions, you can expand the capabilities of Gemini CLI and share those capabilities with others. They are designed to be easily installable and shareable.
+
+## Extension management
+
+We offer a suite of extension management tools using `gemini extensions` commands.
+
+Note that these commands are not supported from within the CLI, although you can list installed extensions using the `/extensions list` subcommand.
+
+Note that all of these commands will only be reflected in active CLI sessions on restart.
+
+### Installing an extension
+
+You can install an extension using `gemini extensions install` with either a GitHub URL source or `--path=some/local/path`.
+
+Note that we create a copy of the installed extension, so you will need to run `gemini extensions update` to pull in changes from both locally-defined extensions and those on GitHub.
+
+```
+gemini extensions install https://github.com/google-gemini/gemini-cli-security
+```
+
+This will install the Gemini CLI Security extension, which offers support for a `/security:analyze` command.
+
+### Uninstalling an extension
+
+To uninstall, run `gemini extensions uninstall extension-name`, so, in the case of the install example:
+
+```
+gemini extensions uninstall gemini-cli-security
+```
+
+### Disabling an extension
+
+Extensions are, by default, enabled across all workspaces. You can disable an extension entirely or for specific workspace.
+
+For example, `gemini extensions disable extension-name` will disable the extension at the user level, so it will be disabled everywhere. `gemini extensions disable extension-name --scope=Workspace` will only disable the extension in the current workspace.
+
+### Enabling an extension
+
+You can re-enable extensions using `gemini extensions enable extension-name`. Note that if an extension is disabled at the user-level, enabling it at the workspace level will not do anything.
+
+### Updating an extension
+
+For extensions installed from a local path or a git repository, you can explicitly update to the latest version (as reflected in the `gemini-extension.json` `version` field) with `gemini extensions update extension-name`.
+
+You can update all extensions with:
+
+```
+gemini extensions update --all
+```
+
+## Extension creation
+
+We offer commands to make extension development easier.
+
+### Create a boilerplate extension
+
+We offer several example extensions `context`, `custom-commands`, `exclude-tools` and `mcp-server`. You can view these examples [here](https://github.com/google-gemini/gemini-cli/tree/main/packages/cli/src/commands/extensions/examples).
+
+To copy one of these examples into a development directory using the type of your choosing, run:
+
+```
+gemini extensions new --path=path/to/directory --type=custom-commands
+```
+
+### Link a local extension
+
+The `gemini extensions link` command will create a symbolic link from the extension installation directory to the development path.
+
+This is useful so you don't have to run `gemini extensions update` every time you make changes you'd like to test.
+
+```
+gemini extensions link path/to/directory
+```
 
 ## How it works
 
-On startup, Gemini CLI looks for extensions in two locations:
+On startup, Gemini CLI looks for extensions in `<home>/.gemini/extensions`
 
-1.  `<workspace>/.gemini/extensions`
-2.  `<home>/.gemini/extensions`
+Extensions exist as a directory that contains a `gemini-extension.json` file. For example:
 
-Gemini CLI loads all extensions from both locations. If an extension with the same name exists in both locations, the extension in the workspace directory takes precedence.
-
-Within each location, individual extensions exist as a directory that contains a `gemini-extension.json` file. For example:
-
-`<workspace>/.gemini/extensions/my-extension/gemini-extension.json`
+`<home>/.gemini/extensions/my-extension/gemini-extension.json`
 
 ### `gemini-extension.json`
 
@@ -33,19 +102,19 @@ The `gemini-extension.json` file contains the configuration for the extension. T
 }
 ```
 
-- `name`: The name of the extension. This is used to uniquely identify the extension and for conflict resolution when extension commands have the same name as user or project commands.
+- `name`: The name of the extension. This is used to uniquely identify the extension and for conflict resolution when extension commands have the same name as user or project commands. The name should be lowercase and use dashes instead of underscores or spaces. This is how users will refer to your extension in the CLI. Note that we expect this name to match the extension directory name.
 - `version`: The version of the extension.
 - `mcpServers`: A map of MCP servers to configure. The key is the name of the server, and the value is the server configuration. These servers will be loaded on startup just like MCP servers configured in a [`settings.json` file](./cli/configuration.md). If both an extension and a `settings.json` file configure an MCP server with the same name, the server defined in the `settings.json` file takes precedence.
-- `contextFileName`: The name of the file that contains the context for the extension. This will be used to load the context from the workspace. If this property is not used but a `GEMINI.md` file is present in your extension directory, then that file will be loaded.
+- `contextFileName`: The name of the file that contains the context for the extension. This will be used to load the context from the extension directory. If this property is not used but a `GEMINI.md` file is present in your extension directory, then that file will be loaded.
 - `excludeTools`: An array of tool names to exclude from the model. You can also specify command-specific restrictions for tools that support it, like the `run_shell_command` tool. For example, `"excludeTools": ["run_shell_command(rm -rf)"]` will block the `rm -rf` command.
 
 When Gemini CLI starts, it loads all the extensions and merges their configurations. If there are any conflicts, the workspace configuration takes precedence.
 
-## Extension Commands
+### Custom commands
 
 Extensions can provide [custom commands](./cli/commands.md#custom-commands) by placing TOML files in a `commands/` subdirectory within the extension directory. These commands follow the same format as user and project custom commands and use standard naming conventions.
 
-### Example
+**Example**
 
 An extension named `gcp` with the following structure:
 
@@ -63,7 +132,7 @@ Would provide these commands:
 - `/deploy` - Shows as `[gcp] Custom command from deploy.toml` in help
 - `/gcs:sync` - Shows as `[gcp] Custom command from sync.toml` in help
 
-### Conflict Resolution
+### Conflict resolution
 
 Extension commands have the lowest precedence. When a conflict occurs with user or project commands:
 
@@ -75,20 +144,7 @@ For example, if both a user and the `gcp` extension define a `deploy` command:
 - `/deploy` - Executes the user's deploy command
 - `/gcp.deploy` - Executes the extension's deploy command (marked with `[gcp]` tag)
 
-## Installing Extensions
-
-You can install extensions using the `install` command. This command allows you to install extensions from a Git repository or a local path.
-
-### Usage
-
-`gemini extensions install <source> | [options]`
-
-### Options
-
-- `source <url> positional argument`: The URL of a Git repository to install the extension from. The repository must contain a `gemini-extension.json` file in its root.
-- `--path <path>`: The path to a local directory to install as an extension. The directory must contain a `gemini-extension.json` file.
-
-# Variables
+## Variables
 
 Gemini CLI extensions allow variable substitution in `gemini-extension.json`. This can be useful if e.g., you need the current directory to run an MCP server using `"cwd": "${extensionPath}${/}run.ts"`.
 

docs/mermaid/context.mmd

@@ -0,0 +1,103 @@
+graph LR
+    %% --- Style Definitions ---
+    classDef new fill:#98fb98,color:#000
+    classDef changed fill:#add8e6,color:#000
+    classDef unchanged fill:#f0f0f0,color:#000
+
+    %% --- Subgraphs ---
+    subgraph "Context Providers"
+        direction TB
+        A["gemini.tsx"]
+        B["AppContainer.tsx"]
+    end
+
+    subgraph "Contexts"
+        direction TB
+        CtxSession["SessionContext"]
+        CtxVim["VimModeContext"]
+        CtxSettings["SettingsContext"]
+        CtxApp["AppContext"]
+        CtxConfig["ConfigContext"]
+        CtxUIState["UIStateContext"]
+        CtxUIActions["UIActionsContext"]
+    end
+
+    subgraph "Component Consumers"
+        direction TB
+        ConsumerApp["App"]
+        ConsumerAppContainer["AppContainer"]
+        ConsumerAppHeader["AppHeader"]
+        ConsumerDialogManager["DialogManager"]
+        ConsumerHistoryItem["HistoryItemDisplay"]
+        ConsumerComposer["Composer"]
+        ConsumerMainContent["MainContent"]
+        ConsumerNotifications["Notifications"]
+    end
+
+    %% --- Provider -> Context Connections ---
+    A -.-> CtxSession
+    A -.-> CtxVim
+    A -.-> CtxSettings
+
+    B -.-> CtxApp
+    B -.-> CtxConfig
+    B -.-> CtxUIState
+    B -.-> CtxUIActions
+    B -.-> CtxSettings
+
+    %% --- Context -> Consumer Connections ---
+    CtxSession -.-> ConsumerAppContainer
+    CtxSession -.-> ConsumerApp
+
+    CtxVim -.-> ConsumerAppContainer
+    CtxVim -.-> ConsumerComposer
+    CtxVim -.-> ConsumerApp
+
+    CtxSettings -.-> ConsumerAppContainer
+    CtxSettings -.-> ConsumerAppHeader
+    CtxSettings -.-> ConsumerDialogManager
+    CtxSettings -.-> ConsumerApp
+
+    CtxApp -.-> ConsumerAppHeader
+    CtxApp -.-> ConsumerNotifications
+
+    CtxConfig -.-> ConsumerAppHeader
+    CtxConfig -.-> ConsumerHistoryItem
+    CtxConfig -.-> ConsumerComposer
+    CtxConfig -.-> ConsumerDialogManager
+
+
+
+    CtxUIState -.-> ConsumerApp
+    CtxUIState -.-> ConsumerMainContent
+    CtxUIState -.-> ConsumerComposer
+    CtxUIState -.-> ConsumerDialogManager
+
+    CtxUIActions -.-> ConsumerComposer
+    CtxUIActions -.-> ConsumerDialogManager
+
+    %% --- Apply Styles ---
+    %% New Elements (Green)
+    class B,CtxApp,CtxConfig,CtxUIState,CtxUIActions,ConsumerAppHeader,ConsumerDialogManager,ConsumerComposer,ConsumerMainContent,ConsumerNotifications new
+
+    %% Heavily Changed Elements (Blue)
+    class A,ConsumerApp,ConsumerAppContainer,ConsumerHistoryItem changed
+
+    %% Mostly Unchanged Elements (Gray)
+    class CtxSession,CtxVim,CtxSettings unchanged
+
+    %% --- Link Styles ---
+    %% CtxSession (Red)
+    linkStyle 0,8,9 stroke:#e57373,stroke-width:2px
+    %% CtxVim (Orange)
+    linkStyle 1,10,11,12 stroke:#ffb74d,stroke-width:2px
+    %% CtxSettings (Yellow)
+    linkStyle 2,7,13,14,15,16 stroke:#fff176,stroke-width:2px
+    %% CtxApp (Green)
+    linkStyle 3,17,18 stroke:#81c784,stroke-width:2px
+    %% CtxConfig (Blue)
+    linkStyle 4,19,20,21,22 stroke:#64b5f6,stroke-width:2px
+    %% CtxUIState (Indigo)
+    linkStyle 5,23,24,25,26 stroke:#7986cb,stroke-width:2px
+    %% CtxUIActions (Violet)
+    linkStyle 6,27,28 stroke:#ba68c8,stroke-width:2px

docs/mermaid/render-path.mmd

@@ -0,0 +1,64 @@
+graph TD
+    %% --- Style Definitions ---
+    classDef new fill:#98fb98,color:#000
+    classDef changed fill:#add8e6,color:#000
+    classDef unchanged fill:#f0f0f0,color:#000
+    classDef dispatcher fill:#f9e79f,color:#000,stroke:#333,stroke-width:1px
+    classDef container fill:#f5f5f5,color:#000,stroke:#ccc
+
+    %% --- Component Tree ---
+    subgraph "Entry Point"
+      A["gemini.tsx"]
+    end
+
+    subgraph "State & Logic Wrapper"
+      B["AppContainer.tsx"]
+    end
+
+    subgraph "Primary Layout"
+      C["App.tsx"]
+    end
+
+    A -.-> B
+    B -.-> C
+
+    subgraph "UI Containers"
+        direction LR
+        C -.-> D["MainContent"]
+        C -.-> G["Composer"]
+        C -.-> F["DialogManager"]
+        C -.-> E["Notifications"]
+    end
+
+    subgraph "MainContent"
+        direction TB
+        D -.-> H["AppHeader"]
+        D -.-> I["HistoryItemDisplay"]:::dispatcher
+        D -.-> L["ShowMoreLines"]
+    end
+
+    subgraph "Composer"
+        direction TB
+        G -.-> K_Prompt["InputPrompt"]
+        G -.-> K_Footer["Footer"]
+    end
+
+    subgraph "DialogManager"
+        F -.-> J["Various Dialogs<br>(Auth, Theme, Settings, etc.)"]
+    end
+
+    %% --- Apply Styles ---
+    class B,D,E,F,G,H,J,K_Prompt,L new
+    class A,C,I changed
+    class K_Footer unchanged
+
+    %% --- Link Styles ---
+    %% MainContent Branch (Blue)
+    linkStyle 2,6,7,8 stroke:#64b5f6,stroke-width:2px
+    %% Composer Branch (Green)
+    linkStyle 3,9,10 stroke:#81c784,stroke-width:2px
+    %% DialogManager Branch (Orange)
+    linkStyle 4,11 stroke:#ffb74d,stroke-width:2px
+    %% Notifications Branch (Violet)
+    linkStyle 5 stroke:#ba68c8,stroke-width:2px
+

docs/sandbox.md

@@ -55,7 +55,9 @@ gemini -p "run the test suite"
 
 # Configure in settings.json
 {
-  "sandbox": "docker"
+  "tools": {
+    "sandbox": "docker"
+  }
 }
 ```
 
@@ -65,7 +67,7 @@ gemini -p "run the test suite"
 
 1. **Command flag**: `-s` or `--sandbox`
 2. **Environment variable**: `GEMINI_SANDBOX=true|docker|podman|sandbox-exec`
-3. **Settings file**: `"sandbox": true` in `settings.json`
+3. **Settings file**: `"sandbox": true` in the `tools` object of your `settings.json` file (e.g., `{"tools": {"sandbox": true}}`).
 
 ### macOS Seatbelt profiles
 

docs/telemetry.md

@@ -47,7 +47,9 @@ The following code can be added to your workspace (`.gemini/settings.json`) or u
     "enabled": true,
     "target": "gcp"
   },
-  "sandbox": false
+  "tools": {
+    "sandbox": false
+  }
 }
 ```
 
@@ -193,6 +195,20 @@ Logs are timestamped records of specific events. The following events are logged
     - `error_type` (if applicable)
     - `metadata` (if applicable, dictionary of string -> any)
 
+- `gemini_cli.file_operation`: This event occurs for each file operation.
+  - **Attributes**:
+    - `tool_name` (string)
+    - `operation` (string: "create", "read", "update")
+    - `lines` (int, if applicable)
+    - `mimetype` (string, if applicable)
+    - `extension` (string, if applicable)
+    - `programming_language` (string, if applicable)
+    - `diff_stat` (json string, if applicable): A JSON string with the following members:
+      - `ai_added_lines` (int)
+      - `ai_removed_lines` (int)
+      - `user_added_lines` (int)
+      - `user_removed_lines` (int)
+
 - `gemini_cli.api_request`: This event occurs when making a request to Gemini API.
   - **Attributes**:
     - `model`
@@ -273,8 +289,8 @@ Metrics are numerical measurements of behavior over time. The following metrics
     - `lines` (Int, if applicable): Number of lines in the file.
     - `mimetype` (string, if applicable): Mimetype of the file.
     - `extension` (string, if applicable): File extension of the file.
-    - `ai_added_lines` (Int, if applicable): Number of lines added/changed by AI.
-    - `ai_removed_lines` (Int, if applicable): Number of lines removed/changed by AI.
+    - `model_added_lines` (Int, if applicable): Number of lines added/changed by the model.
+    - `model_removed_lines` (Int, if applicable): Number of lines removed/changed by the model.
     - `user_added_lines` (Int, if applicable): Number of lines added/changed by user in AI proposed changes.
     - `user_removed_lines` (Int, if applicable): Number of lines removed/changed by user in AI proposed changes.
     - `programming_language` (string, if applicable): The programming language of the file.

docs/tools/mcp-server.md

@@ -51,7 +51,30 @@ The Gemini CLI uses the `mcpServers` configuration in your `settings.json` file
 
 ### Configure the MCP server in settings.json
 
-You can configure MCP servers at the global level in the `~/.gemini/settings.json` file or in your project's root directory, create or open the `.gemini/settings.json` file. Within the file, add the `mcpServers` configuration block.
+You can configure MCP servers in your `settings.json` file in two main ways: through the top-level `mcpServers` object for specific server definitions, and through the `mcp` object for global settings that control server discovery and execution.
+
+#### Global MCP Settings (`mcp`)
+
+The `mcp` object in your `settings.json` allows you to define global rules for all MCP servers.
+
+- **`mcp.serverCommand`** (string): A global command to start an MCP server.
+- **`mcp.allowed`** (array of strings): A list of MCP server names to allow. If this is set, only servers from this list (matching the keys in the `mcpServers` object) will be connected to.
+- **`mcp.excluded`** (array of strings): A list of MCP server names to exclude. Servers in this list will not be connected to.
+
+**Example:**
+
+```json
+{
+  "mcp": {
+    "allowed": ["my-trusted-server"],
+    "excluded": ["experimental-server"]
+  }
+}
+```
+
+#### Server-Specific Configuration (`mcpServers`)
+
+The `mcpServers` object is where you define each individual MCP server you want the CLI to connect to.
 
 ### Configuration Structure
 
@@ -92,7 +115,7 @@ Each server configuration supports the following properties:
 - **`cwd`** (string): Working directory for Stdio transport
 - **`timeout`** (number): Request timeout in milliseconds (default: 600,000ms = 10 minutes)
 - **`trust`** (boolean): When `true`, bypasses all tool call confirmations for this server (default: `false`)
-- **`includeTools`** (string[]): List of tool names to include from this MCP server. When specified, only the tools listed here will be available from this server (whitelist behavior). If not specified, all tools from the server are enabled by default.
+- **`includeTools`** (string[]): List of tool names to include from this MCP server. When specified, only the tools listed here will be available from this server (allowlist behavior). If not specified, all tools from the server are enabled by default.
 - **`excludeTools`** (string[]): List of tool names to exclude from this MCP server. Tools listed here will not be available to the model, even if they are exposed by the server. **Note:** `excludeTools` takes precedence over `includeTools` - if a tool is in both lists, it will be excluded.
 
 ### OAuth Support for Remote MCP Servers
@@ -667,9 +690,13 @@ await server.connect(transport);
 This can be included in `settings.json` under `mcpServers` with:
 
 ```json
-"nodeServer": {
-  "command": "node",
-  "args": ["filename.ts"],
+{
+  "mcpServers": {
+    "nodeServer": {
+      "command": "node",
+      "args": ["filename.ts"]
+    }
+  }
 }
 ```
 

docs/tools/shell.md

@@ -66,16 +66,16 @@ When `run_shell_command` executes a command, it sets the `GEMINI_CLI=1` environm
 
 ## Command Restrictions
 
-You can restrict the commands that can be executed by the `run_shell_command` tool by using the `coreTools` and `excludeTools` settings in your configuration file.
+You can restrict the commands that can be executed by the `run_shell_command` tool by using the `tools.core` and `tools.exclude` settings in your configuration file.
 
-- `coreTools`: To restrict `run_shell_command` to a specific set of commands, add entries to the `coreTools` list in the format `run_shell_command(<command>)`. For example, `"coreTools": ["run_shell_command(git)"]` will only allow `git` commands. Including the generic `run_shell_command` acts as a wildcard, allowing any command not explicitly blocked.
-- `excludeTools`: To block specific commands, add entries to the `excludeTools` list in the format `run_shell_command(<command>)`. For example, `"excludeTools": ["run_shell_command(rm)"]` will block `rm` commands.
+- `tools.core`: To restrict `run_shell_command` to a specific set of commands, add entries to the `core` list under the `tools` category in the format `run_shell_command(<command>)`. For example, `"tools": {"core": ["run_shell_command(git)"]}` will only allow `git` commands. Including the generic `run_shell_command` acts as a wildcard, allowing any command not explicitly blocked.
+- `tools.exclude`: To block specific commands, add entries to the `exclude` list under the `tools` category in the format `run_shell_command(<command>)`. For example, `"tools": {"exclude": ["run_shell_command(rm)"]}` will block `rm` commands.
 
 The validation logic is designed to be secure and flexible:
 
 1.  **Command Chaining Disabled**: The tool automatically splits commands chained with `&&`, `||`, or `;` and validates each part separately. If any part of the chain is disallowed, the entire command is blocked.
 2.  **Prefix Matching**: The tool uses prefix matching. For example, if you allow `git`, you can run `git status` or `git log`.
-3.  **Blocklist Precedence**: The `excludeTools` list is always checked first. If a command matches a blocked prefix, it will be denied, even if it also matches an allowed prefix in `coreTools`.
+3.  **Blocklist Precedence**: The `tools.exclude` list is always checked first. If a command matches a blocked prefix, it will be denied, even if it also matches an allowed prefix in `tools.core`.
 
 ### Command Restriction Examples
 
@@ -85,7 +85,9 @@ To allow only `git` and `npm` commands, and block all others:
 
 ```json
 {
-  "coreTools": ["run_shell_command(git)", "run_shell_command(npm)"]
+  "tools": {
+    "core": ["run_shell_command(git)", "run_shell_command(npm)"]
+  }
 }
 ```
 
@@ -99,8 +101,10 @@ To block `rm` and allow all other commands:
 
 ```json
 {
-  "coreTools": ["run_shell_command"],
-  "excludeTools": ["run_shell_command(rm)"]
+  "tools": {
+    "core": ["run_shell_command"],
+    "exclude": ["run_shell_command(rm)"]
+  }
 }
 ```
 
@@ -110,12 +114,14 @@ To block `rm` and allow all other commands:
 
 **Blocklist takes precedence**
 
-If a command prefix is in both `coreTools` and `excludeTools`, it will be blocked.
+If a command prefix is in both `tools.core` and `tools.exclude`, it will be blocked.
 
 ```json
 {
-  "coreTools": ["run_shell_command(git)"],
-  "excludeTools": ["run_shell_command(git push)"]
+  "tools": {
+    "core": ["run_shell_command(git)"],
+    "exclude": ["run_shell_command(git push)"]
+  }
 }
 ```
 
@@ -124,11 +130,13 @@ If a command prefix is in both `coreTools` and `excludeTools`, it will be blocke
 
 **Block all shell commands**
 
-To block all shell commands, add the `run_shell_command` wildcard to `excludeTools`:
+To block all shell commands, add the `run_shell_command` wildcard to `tools.exclude`:
 
 ```json
 {
-  "excludeTools": ["run_shell_command"]
+  "tools": {
+    "exclude": ["run_shell_command"]
+  }
 }
 ```
 

docs/troubleshooting.md

@@ -72,7 +72,7 @@ This guide provides solutions to common issues and debugging tips, including top
 - **DEBUG mode not working from project .env file**
   - **Issue:** Setting `DEBUG=true` in a project's `.env` file doesn't enable debug mode for gemini-cli.
   - **Cause:** The `DEBUG` and `DEBUG_MODE` variables are automatically excluded from project `.env` files to prevent interference with gemini-cli behavior.
-  - **Solution:** Use a `.gemini/.env` file instead, or configure the `excludedProjectEnvVars` setting in your `settings.json` to exclude fewer variables.
+  - **Solution:** Use a `.gemini/.env` file instead, or configure the `advanced.excludedEnvVars` setting in your `settings.json` to exclude fewer variables.
 
 ## Exit Codes
 

esbuild.config.js

@@ -8,12 +8,23 @@ import esbuild from 'esbuild';
 import path from 'node:path';
 import { fileURLToPath } from 'node:url';
 import { createRequire } from 'node:module';
+import { writeFileSync } from 'node:fs';
 
 const __filename = fileURLToPath(import.meta.url);
 const __dirname = path.dirname(__filename);
 const require = createRequire(import.meta.url);
 const pkg = require(path.resolve(__dirname, 'package.json'));
 
+const external = [
+  '@lydell/node-pty',
+  'node-pty',
+  '@lydell/node-pty-darwin-arm64',
+  '@lydell/node-pty-darwin-x64',
+  '@lydell/node-pty-linux-x64',
+  '@lydell/node-pty-win32-arm64',
+  '@lydell/node-pty-win32-x64',
+];
+
 esbuild
   .build({
     entryPoints: ['packages/cli/index.ts'],
@@ -21,15 +32,7 @@ esbuild
     outfile: 'bundle/gemini.js',
     platform: 'node',
     format: 'esm',
-    external: [
-      '@lydell/node-pty',
-      'node-pty',
-      '@lydell/node-pty-darwin-arm64',
-      '@lydell/node-pty-darwin-x64',
-      '@lydell/node-pty-linux-x64',
-      '@lydell/node-pty-win32-arm64',
-      '@lydell/node-pty-win32-x64',
-    ],
+    external,
     alias: {
       'is-in-ci': path.resolve(
         __dirname,
@@ -43,5 +46,12 @@ esbuild
       js: `import { createRequire } from 'module'; const require = createRequire(import.meta.url); globalThis.__filename = require('url').fileURLToPath(import.meta.url); globalThis.__dirname = require('path').dirname(globalThis.__filename);`,
     },
     loader: { '.node': 'file' },
+    metafile: true,
+    write: true,
+  })
+  .then(({ metafile }) => {
+    if (process.env.DEV === 'true') {
+      writeFileSync('./bundle/esbuild.json', JSON.stringify(metafile, null, 2));
+    }
   })
   .catch(() => process.exit(1));

integration-tests/read_many_files.test.ts

@@ -14,7 +14,7 @@ describe('read_many_files', () => {
     rig.createFile('file1.txt', 'file 1 content');
     rig.createFile('file2.txt', 'file 2 content');
 
-    const prompt = `Please use read_many_files to read file1.txt and file2.txt and show me what's in them`;
+    const prompt = `Use the read_many_files tool to read the contents of file1.txt and file2.txt and then print the contents of each file.`;
 
     const result = await rig.run(prompt);
 
@@ -41,11 +41,7 @@ describe('read_many_files', () => {
       'Expected to find either read_many_files or multiple read_file tool calls',
     ).toBeTruthy();
 
-    // Validate model output - will throw if no output, warn if missing expected content
-    validateModelOutput(
-      result,
-      ['file 1 content', 'file 2 content'],
-      'Read many files test',
-    );
+    // Validate model output - will throw if no output
+    validateModelOutput(result, null, 'Read many files test');
   });
 });

integration-tests/session-summary.test.ts

@@ -0,0 +1,37 @@
+/**
+ * @license
+ * Copyright 2025 Google LLC
+ * SPDX-License-Identifier: Apache-2.0
+ */
+
+import { TestRig } from './test-helper.js';
+import { describe, it, expect, beforeEach, afterEach } from 'vitest';
+import { join } from 'node:path';
+import { readFileSync } from 'node:fs';
+
+describe('session-summary flag', () => {
+  let rig: TestRig;
+
+  beforeEach(function (context) {
+    rig = new TestRig();
+    if (context.task.name) {
+      rig.setup(context.task.name);
+    }
+  });
+
+  afterEach(async () => {
+    await rig.cleanup();
+  });
+
+  it('should write a session summary in non-interactive mode', async () => {
+    const summaryPath = join(rig.testDir!, 'summary.json');
+    await rig.run('Say hello', '--session-summary', summaryPath);
+
+    const summaryContent = readFileSync(summaryPath, 'utf-8');
+    const summary = JSON.parse(summaryContent);
+
+    expect(summary).toBeDefined();
+    expect(summary.sessionMetrics.models).toBeDefined();
+    expect(summary.sessionMetrics.tools).toBeDefined();
+  });
+});

integration-tests/shell-service.test.ts

@@ -96,8 +96,8 @@ describe('ShellExecutionService programmatic integration tests', () => {
   );
 
   it('should abort a running process', async () => {
-    // A command that runs for a bit. 'sleep' on unix, 'timeout' on windows.
-    const command = process.platform === 'win32' ? 'timeout /t 20' : 'sleep 20';
+    // A command that runs for a bit.
+    const command = 'node -e "setTimeout(() => {}, 20000)"';
     const onOutputEvent = vi.fn();
     const abortController = new AbortController();
 

integration-tests/test-helper.ts

@@ -5,7 +5,6 @@
  */
 
 import { execSync, spawn } from 'node:child_process';
-import { parse } from 'shell-quote';
 import { mkdirSync, writeFileSync, readFileSync } from 'node:fs';
 import { join, dirname } from 'node:path';
 import { fileURLToPath } from 'node:url';
@@ -182,7 +181,7 @@ export class TestRig {
       | { prompt?: string; stdin?: string; stdinDoesNotEnd?: boolean },
     ...args: string[]
   ): Promise<string> {
-    let command = `node ${this.bundlePath} --yolo`;
+    const commandArgs = [this.bundlePath, '--yolo'];
     const execOptions: {
       cwd: string;
       encoding: 'utf-8';
@@ -193,25 +192,22 @@ export class TestRig {
     };
 
     if (typeof promptOrOptions === 'string') {
-      command += ` --prompt ${JSON.stringify(promptOrOptions)}`;
+      commandArgs.push('--prompt', promptOrOptions);
     } else if (
       typeof promptOrOptions === 'object' &&
       promptOrOptions !== null
     ) {
       if (promptOrOptions.prompt) {
-        command += ` --prompt ${JSON.stringify(promptOrOptions.prompt)}`;
+        commandArgs.push('--prompt', promptOrOptions.prompt);
       }
       if (promptOrOptions.stdin) {
         execOptions.input = promptOrOptions.stdin;
       }
     }
 
-    command += ` ${args.join(' ')}`;
+    commandArgs.push(...args);
 
-    const commandArgs = parse(command);
-    const node = commandArgs.shift() as string;
-
-    const child = spawn(node, commandArgs as string[], {
+    const child = spawn('node', commandArgs, {
       cwd: this.testDir!,
       stdio: 'pipe',
     });

integration-tests/utf-bom-encoding.test.ts

@@ -0,0 +1,141 @@
+/**
+ * @license
+ * Copyright 2025 Google LLC
+ * SPDX-License-Identifier: Apache-2.0
+ */
+
+import { describe, it, expect, beforeAll, afterAll } from 'vitest';
+import { writeFileSync, readFileSync } from 'node:fs';
+import { join, resolve } from 'node:path';
+import { TestRig } from './test-helper.js';
+
+// Windows skip (Option A: avoid infra scope)
+const d = process.platform === 'win32' ? describe.skip : describe;
+
+// BOM encoders
+const utf8BOM = (s: string) =>
+  Buffer.concat([Buffer.from([0xef, 0xbb, 0xbf]), Buffer.from(s, 'utf8')]);
+const utf16LE = (s: string) =>
+  Buffer.concat([Buffer.from([0xff, 0xfe]), Buffer.from(s, 'utf16le')]);
+const utf16BE = (s: string) => {
+  const bom = Buffer.from([0xfe, 0xff]);
+  const le = Buffer.from(s, 'utf16le');
+  le.swap16();
+  return Buffer.concat([bom, le]);
+};
+const utf32LE = (s: string) => {
+  const bom = Buffer.from([0xff, 0xfe, 0x00, 0x00]);
+  const cps = Array.from(s, (c) => c.codePointAt(0)!);
+  const payload = Buffer.alloc(cps.length * 4);
+  cps.forEach((cp, i) => {
+    const o = i * 4;
+    payload[o] = cp & 0xff;
+    payload[o + 1] = (cp >>> 8) & 0xff;
+    payload[o + 2] = (cp >>> 16) & 0xff;
+    payload[o + 3] = (cp >>> 24) & 0xff;
+  });
+  return Buffer.concat([bom, payload]);
+};
+const utf32BE = (s: string) => {
+  const bom = Buffer.from([0x00, 0x00, 0xfe, 0xff]);
+  const cps = Array.from(s, (c) => c.codePointAt(0)!);
+  const payload = Buffer.alloc(cps.length * 4);
+  cps.forEach((cp, i) => {
+    const o = i * 4;
+    payload[o] = (cp >>> 24) & 0xff;
+    payload[o + 1] = (cp >>> 16) & 0xff;
+    payload[o + 2] = (cp >>> 8) & 0xff;
+    payload[o + 3] = cp & 0xff;
+  });
+  return Buffer.concat([bom, payload]);
+};
+
+let rig: TestRig;
+let dir: string;
+
+d('BOM end-to-end integration', () => {
+  beforeAll(async () => {
+    rig = new TestRig();
+    await rig.setup('bom-integration');
+    dir = rig.testDir!;
+  });
+
+  afterAll(async () => {
+    await rig.cleanup();
+  });
+
+  async function runAndAssert(
+    filename: string,
+    content: Buffer,
+    expectedText: string | null,
+  ) {
+    writeFileSync(join(dir, filename), content);
+    const prompt = `read the file ${filename} and output its exact contents`;
+    const output = await rig.run(prompt);
+    await rig.waitForToolCall('read_file');
+    const lower = output.toLowerCase();
+    if (expectedText === null) {
+      expect(
+        lower.includes('binary') ||
+          lower.includes('skipped binary file') ||
+          lower.includes('cannot display'),
+      ).toBeTruthy();
+    } else {
+      expect(output.includes(expectedText)).toBeTruthy();
+      expect(lower.includes('skipped binary file')).toBeFalsy();
+    }
+  }
+
+  it('UTF-8 BOM', async () => {
+    await runAndAssert('utf8.txt', utf8BOM('BOM_OK UTF-8'), 'BOM_OK UTF-8');
+  });
+
+  it('UTF-16 LE BOM', async () => {
+    await runAndAssert(
+      'utf16le.txt',
+      utf16LE('BOM_OK UTF-16LE'),
+      'BOM_OK UTF-16LE',
+    );
+  });
+
+  it('UTF-16 BE BOM', async () => {
+    await runAndAssert(
+      'utf16be.txt',
+      utf16BE('BOM_OK UTF-16BE'),
+      'BOM_OK UTF-16BE',
+    );
+  });
+
+  it('UTF-32 LE BOM', async () => {
+    await runAndAssert(
+      'utf32le.txt',
+      utf32LE('BOM_OK UTF-32LE'),
+      'BOM_OK UTF-32LE',
+    );
+  });
+
+  it('UTF-32 BE BOM', async () => {
+    await runAndAssert(
+      'utf32be.txt',
+      utf32BE('BOM_OK UTF-32BE'),
+      'BOM_OK UTF-32BE',
+    );
+  });
+
+  it('Can describe a PNG file', async () => {
+    const imagePath = resolve(
+      process.cwd(),
+      'docs/assets/gemini-screenshot.png',
+    );
+    const imageContent = readFileSync(imagePath);
+    const filename = 'gemini-screenshot.png';
+    writeFileSync(join(dir, filename), imageContent);
+    const prompt = `What is shown in the image ${filename}?`;
+    const output = await rig.run(prompt);
+    await rig.waitForToolCall('read_file');
+    const lower = output.toLowerCase();
+    // The response is non-deterministic, so we just check for some
+    // keywords that are very likely to be in the response.
+    expect(lower.includes('gemini')).toBeTruthy();
+  });
+});

package.json

@@ -1,6 +1,6 @@
 {
   "name": "@google/gemini-cli",
-  "version": "0.3.2",
+  "version": "0.5.3",
   "engines": {
     "node": ">=20.0.0"
   },
@@ -14,7 +14,7 @@
     "url": "git+https://github.com/google-gemini/gemini-cli.git"
   },
   "config": {
-    "sandboxImageUri": "us-docker.pkg.dev/gemini-code-dev/gemini-cli/sandbox:0.3.2"
+    "sandboxImageUri": "us-docker.pkg.dev/gemini-code-dev/gemini-cli/sandbox:0.5.3"
   },
   "scripts": {
     "start": "node scripts/start.js",
@@ -36,9 +36,9 @@
     "test:scripts": "vitest run --config ./scripts/tests/vitest.config.ts",
     "test:e2e": "cross-env VERBOSE=true KEEP_OUTPUT=true npm run test:integration:sandbox:none",
     "test:integration:all": "npm run test:integration:sandbox:none && npm run test:integration:sandbox:docker && npm run test:integration:sandbox:podman",
-    "test:integration:sandbox:none": "GEMINI_SANDBOX=false vitest run --root ./integration-tests",
-    "test:integration:sandbox:docker": "GEMINI_SANDBOX=docker npm run build:sandbox && GEMINI_SANDBOX=docker vitest run --root ./integration-tests",
-    "test:integration:sandbox:podman": "GEMINI_SANDBOX=podman vitest run --root ./integration-tests",
+    "test:integration:sandbox:none": "cross-env GEMINI_SANDBOX=false vitest run --root ./integration-tests",
+    "test:integration:sandbox:docker": "cross-env GEMINI_SANDBOX=docker npm run build:sandbox && cross-env GEMINI_SANDBOX=docker vitest run --root ./integration-tests",
+    "test:integration:sandbox:podman": "cross-env GEMINI_SANDBOX=podman vitest run --root ./integration-tests",
     "lint": "eslint . --ext .ts,.tsx && eslint integration-tests",
     "lint:fix": "eslint . --fix && eslint integration-tests --fix",
     "lint:ci": "eslint . --ext .ts,.tsx --max-warnings 0 && eslint integration-tests --max-warnings 0",
@@ -49,6 +49,7 @@
     "prepare:package": "node scripts/prepare-package.js",
     "release:version": "node scripts/version.js",
     "telemetry": "node scripts/telemetry.js",
+    "check:lockfile": "node scripts/check-lockfile.js",
     "clean": "node scripts/clean.js"
   },
   "bin": {
@@ -67,7 +68,6 @@
     "@types/shell-quote": "^1.7.5",
     "@vitest/coverage-v8": "^3.1.1",
     "@vitest/eslint-plugin": "^1.3.4",
-    "concurrently": "^9.2.0",
     "cross-env": "^7.0.3",
     "esbuild": "^0.25.0",
     "eslint": "^9.24.0",
@@ -79,7 +79,6 @@
     "glob": "^10.4.5",
     "globals": "^16.0.0",
     "json": "^11.0.0",
-    "lodash": "^4.17.21",
     "memfs": "^4.17.2",
     "mnemonist": "^0.40.3",
     "mock-fs": "^5.5.0",
@@ -92,9 +91,7 @@
     "yargs": "^17.7.2"
   },
   "dependencies": {
-    "@lvce-editor/ripgrep": "^1.6.0",
-    "simple-git": "^3.28.0",
-    "strip-ansi": "^7.1.0"
+    "simple-git": "^3.28.0"
   },
   "optionalDependencies": {
     "@lydell/node-pty": "1.1.0",

packages/a2a-server/development-extension-rfc.md

@@ -0,0 +1,418 @@
+# RFC: Gemini CLI A2A Development-Tool Extension
+
+## 1. Introduction
+
+### 1.1 Overview
+
+To standardize client integrations with the Gemini CLI agent, this document proposes the `development-tool` extension for the A2A protocol.
+
+Rather than creating a new protocol, this specification builds upon the existing A2A protocol. As an open-source standard recently adopted by the Linux Foundation, A2A provides a robust foundation for core concepts like tasks, messages, and streaming events. This extension-based approach allows us to leverage A2A's proven architecture while defining the specific capabilities required for rich, interactive workflows with the Gemini CLI agent.
+
+### 1.2 Motivation
+
+Recent work integrating Gemini CLI with clients like Zed and Gemini Code Assist’s agent mode has highlighted the need for a robust, standard communication protocol. Standardizing on A2A provides several key advantages:
+
+- **Solid Foundation**: Provides a robust, open standard that ensures a stable, predictable, and consistent integration experience across different IDEs and client surfaces.
+- **Extensibility**: Creates a flexible foundation to support new tools and workflows as they emerge.
+- **Ecosystem Alignment**: Aligns Gemini CLI with a growing industry standard, fostering broader interoperability.
+
+## 2. Communication Flow
+
+The interaction follows A2A’s task-based, streaming pattern. The client sends a `message/stream` request and the agent responds with a `contextId` / `taskId` and a stream of events. `TaskStatusUpdateEvent` events are used to convey the overall state of the task. The task is complete when the agent sends a final `TaskStatusUpdateEvent` with `final: true` and a terminal status like `completed` or `failed`.
+
+### 2.1 Asynchronous Responses and Notifications
+
+Clients that may disconnect from the agent should supply a `PushNotificationConfig` to the agent with the initial `message/stream` method or subsequently with the `tasks/pushNotificationConfig/set` method so that the agent can call back when updates are ready.
+
+## 3. The `development-tool` extension
+
+### 3.1 Overview
+
+The `development-tool` extension establishes a communication contract for workflows between a client and the Gemini CLI agent. It consists of a specialized set of schemas, embedded within core A2A data structures, that enable the agent to stream real-time updates on its state and thought process. These schemas also provide the mechanism for the agent to request user permission before executing tools.
+
+**Sample Agent Card**
+
+```json
+{
+  "name": "Gemini CLI Agent",
+  "description": "An agent that generates code based on natural language instructions.",
+  "capabilities": {
+    "streaming": true,
+    "extensions": [
+      {
+        "uri": "https://github.com/google-gemini/gemini-cli/blob/main/docs/a2a/developer-profile/v0/spec.md",
+        "description": "An extension for interactive development tasks, enabling features like code generation, tool usage, and real-time status updates.",
+        "required": true
+      }
+    ]
+  }
+}
+```
+
+**Versioning**
+
+The agent card `uri` field contains an embedded semantic version. The client must extract this version to determine compatibility with the agent extension using the compatibility logic defined in Semantic Versioning 2.0.0 spec.
+
+### 3.2 Schema Definitions
+
+This section defines the schemas for the `development-tool` A2A extension, organized by their function within the communication flow. Note that all custom objects included in the `metadata` field (e.g. `Message.metadata`) must be keyed by the unique URI that points to that extension’s spec to prevent naming collisions with other extensions.
+
+**Initialization & Configuration**
+
+The first message in a session must contain an `AgentSettings` object in its metadata. This object provides the agent with the necessary configuration information for proper initialization. Additional configuration settings (ex. MCP servers, allowed tools, etc.) can be added to this message.
+
+**Schema**
+
+```proto
+syntax = "proto3";
+
+// Configuration settings for the Gemini CLI agent.
+message AgentSettings {
+  // The absolute path to the workspace directory where the agent will execute.
+  string workspace_path = 1;
+}
+```
+
+**Agent-to-Client Messages**
+
+All real-time updates from the agent (including its thoughts, tool calls, and simple text replies) are streamed to the client as `TaskStatusUpdateEvents`.
+
+Each Event contains a `Message` object, which holds the content in one of two formats:
+
+- **TextPart**: Used for standard text messages. This part requires no custom schema.
+- **DataPart**: Used for complex, structured objects. Tool Calls and Thoughts are sent this way, each using their respective schemas defined below.
+
+**Tool Calls**
+
+The `ToolCall` schema is designed to provide a structured representation of a tool’s execution lifecycle. This protocol defines a clear state machine and provides detailed schemas for common development tasks (file edits, shell commands, MCP Tool), ensuring clients can build reliable UIs without being tied to a specific agent implementation.
+
+The core principle is that the agent sends a `ToolCall` object on every update. This makes client-side logic stateless and simple.
+
+**Tool Call Lifecycle**
+
+1.  **Creation**: The agent sends a `ToolCall` object with `status: PENDING`. If user permission is required, the `confirmation_request` field will be populated.
+2.  **Confirmation**: If the client needs to confirm the message, the client will send a `ToolCallConfirmation`. If the client responds with a cancellation, execution will be skipped.
+3.  **Execution**: Once approved (or if no approval is required), the agent sends an update with `status: EXECUTING`. It can stream real-time progress by updating the `live_content` field.
+4.  **Completion**: The agent sends a final update with the status set to `SUCCEEDED`, `FAILED`, or `CANCELLED` and populates the appropriate result field.
+
+**Schema**
+
+```proto
+syntax = "proto3";
+
+import "google/protobuf/struct.proto";
+
+// ToolCall is the central message represeting a tool's execution lifecycle.
+// The entire object is sent from the agent to client on every update.
+message ToolCall {
+  // A unique identifier, assigned by the agent
+  string tool_call_id = 1;
+
+  // The current state of the tool call in its lifecycle
+  ToolCallStatus status = 2;
+
+  // Name of the tool being called (e.g. 'Edit', 'ShellTool')
+  string tool_name = 3;
+
+  // An optional description of the tool call's purpose to show the user
+  optional string description = 4;
+
+  // The structured input params provided by the LLM for tool invocation.
+  google.protobuf.Struct input_parameters = 5;
+
+  // String containing the real-time output from the tool as it executes (primarily designed for shell output).
+  // During streaming the entire string is replaced on each update
+  optional string live_content = 6;
+
+  // The final result of the tool (used to replace live_content when applicable)
+  oneof result {
+    // The output on tool success
+    ToolOutput output = 7;
+    // The error details if the tool failed
+    ErrorDetails error = 8;
+  }
+
+  // If the tool requires user confirmation, this field will be populated while status is PENDING
+  optional ConfirmationRequest confirmation_request = 9;
+}
+
+// Possible execution status of a ToolCall
+enum ToolCallStatus {
+  STATUS_UNSPECIFIED = 0;
+  PENDING = 1;
+  EXECUTING = 2;
+  SUCCEEDED = 3;
+  FAILED = 4;
+  CANCELLED = 5;
+}
+
+// ToolOuput represents the final, successful, output of a tool
+message ToolOutput {
+  oneof result {
+    string text = 1;
+    // For ToolCalls which resulted in a file modification
+    FileDiff diff = 2;
+    // A generic fallback for any other structured JSON data
+    google.protobuf.Struct structured_data = 3;
+  }
+}
+
+// A structured representation of an error
+message ErrorDetails {
+  // User facing error message
+  string message = 1;
+  // Optional agent-specific error type or category (e.g. read_content_failure, grep_execution_error, mcp_tool_error)
+  optional string type = 2;
+  // Optional status code
+  optional int32 status_code = 3;
+}
+
+// ConfirmationRequest is sent from the agent to client to request user permission for a ToolCall
+message ConfirmationRequest {
+  // A list of choices for the user to select from
+  repeated ConfirmationOption options = 1;
+  // Specific details of the action requiring user confirmation
+  oneof details {
+    ExecuteDetails execute_details = 2;
+    FileDiff file_edit_details = 3;
+    McpDetails mcp_details = 4;
+    GenericDetails generic_details = 5;
+  }
+}
+
+// A single choice presented to the user during a confirmation request
+message ConfirmationOption {
+  // Unique ID for the choice (e.g. proceed_once, cancel)
+  string id = 1;
+  // Human-readable choice (e.g. Allow Once, Reject).
+  string name = 2;
+  // An optional longer description for a tooltip
+  optional string description = 3;
+}
+
+// Details for a request to execute a shell command
+message ExecuteDetails {
+  // The shell command to be executed
+  string command = 1;
+  // An optional directory in which the command will be run
+  optional string working_directory = 2;
+}
+
+
+message FileDiff {
+  string file_name = 1;
+  // The absolute path to the file to modify
+  string file_path = 2;
+  // The original content, if the file exists
+  optional string old_content = 3;
+  string new_content = 4;
+  // Pre-formatted diff string for display
+  optional string formatted_diff = 5;
+}
+
+// Details for an MCP (Model Context Protocol) tool confirmation
+message McpDetails {
+  // The name of the MCP server that provides the tool
+  string server_name = 1;
+  // THe name of the tool being called from the MCP Server
+  string tool_name = 2;
+}
+
+// Generic catch-all for ToolCall requests that don't fit other types
+message GenericDetails {
+  // Description of the action requiring confirmation
+  string description = 1;
+}
+```
+
+**Agent Thoughts**
+
+**Schema**
+
+```proto
+syntax = "proto3";
+
+// Represents a thought with a subject and a detailed description.
+message AgentThought {
+  // A concise subject line or title for the thought.
+  string subject = 1;
+
+  // The description or elaboration of the thought itself.
+  string description = 2;
+}
+```
+
+**Event Metadata**
+
+The `metadata` object in `TaskStatusUpdateEvent` is used by the A2A client to deserialize the `TaskStatusUpdateEvents` into their appropriate objects.
+
+**Schema**
+
+```proto
+syntax = "proto3";
+
+// A DevelopmentToolEvent event.
+message DevelopmentToolEvent {
+  // Enum representing the specific type of development tool event.
+  enum DevelopmentToolEventKind {
+    // The default, unspecified value.
+    DEVELOPMENT_TOOL_EVENT_KIND_UNSPECIFIED = 0;
+    TOOL_CALL_CONFIRMATION = 1;
+    TOOL_CALL_UPDATE = 2;
+    TEXT_CONTENT = 3;
+    STATE_CHANGE = 4;
+    THOUGHT = 5;
+  }
+
+  // The specific kind of event that occurred.
+  DevelopmentToolEventKind kind = 1;
+
+  // The model used for this event.
+  string model = 2;
+
+  // The tier of the user (optional).
+  string user_tier = 3;
+
+  // An unexpected error occured in the agent execution (optional).
+  string error = 4;
+}
+```
+
+**Client-to-Agent Messages**
+
+When the agent sends a `TaskStatusUpdateEvent` with `status.state` set to `input-required` and its message contains a `ConfirmationRequest`, the client must respond by sending a new `message/stream` request.
+
+This new request must include the `contextId` and the `taskId` from the ongoing task and contain a `ToolCallConfirmation` object. This object conveys the user's decision regarding the tool call that was awaiting approval.
+
+**Schema**
+
+```proto
+syntax = "proto3";
+
+// The client's response to a ConfirmationRequest.
+message ToolCallConfirmation {
+  // A unique identifier, assigned by the agent
+  string tool_call_id = 1;
+  // The 'id' of the ConfirmationOption chosen by the user.
+  string selected_option_id = 2;
+  // Included if the user modifies the proposed change.
+  // The type should correspond to the original ConfirmationRequest details.
+  oneof modified_details {
+    // Corresponds to a FileDiff confirmation
+    ModifiedFileDetails file_details = 3;
+  }
+}
+
+message ModifiedFileDetails {
+  // The new content after user edits.
+  string new_content = 1;
+}
+```
+
+### 3.3 Method Definitions
+
+This section defines the new methods introduced by the `development-tool` extension.
+
+**Method: `commands/get`**
+
+This method allows the client to discover slash commands supported by Gemini CLI. The client should call this method during startup to dynamically populate its command list.
+
+```proto
+// Response message containing the list of all top-level slash commands.
+message GetAllSlashCommandsResponse {
+  // A list of the top-level slash commands.
+  repeated SlashCommand commands = 1;
+}
+
+// Represents a single slash command, which can contain subcommands.
+message SlashCommand {
+  // The primary name of the command.
+  string name = 1;
+  // A detailed description of what the command does.
+  string description = 2;
+  // A list of arguments that the command accepts.
+  repeated SlashCommandArgument arguments = 3;
+  // A list of nested subcommands.
+  repeated SlashCommand sub_commands = 4;
+}
+
+// Defines the structure for a single slash command argument.
+message SlashCommandArgument {
+  // The name of the argument.
+  string name = 1;
+  // A brief description of what the argument is for.
+  string description = 2;
+  // Whether the argument is required or optional.
+  bool is_required = 3;
+}
+```
+
+**Method: `command/execute`**
+
+This method allows the client to execute a slash command. Following the initial `ExecuteSlashCommandResponse`, the agent will use the standard streaming mechanism to communicate the command's progress and output. All subsequent updates, including textual output, agent thoughts, and any required user confirmations for tool calls (like executing a shell command), will be sent as `TaskStatusUpdateEvent` messages, re-using the schemas defined above.
+
+```proto
+// Request to execute a specific slash command.
+message ExecuteSlashCommandRequest {
+  // The path to the command, e.g., ["memory", "add"] for /memory add
+  repeated string command_path = 1;
+  // The arguments for the command as a single string.
+  string args = 2;
+}
+
+// Enum for the initial status of a command execution request.
+enum CommandExecutionStatus {
+  // Default unspecified status.
+  COMMAND_EXECUTION_STATUS_UNSPECIFIED = 0;
+  // The command was successfully received and its execution has started.
+  STARTED = 1;
+  // The command failed to start (e.g., command not found, invalid format).
+  FAILED_TO_START = 2;
+  // The command has been paused and is waiting for the user to confirm
+  // a set of shell commands.
+  AWAITING_SHELL_CONFIRMATION = 3;
+  // The command has been paused and is waiting for the user to confirm
+  // a specific action.
+  AWAITING_ACTION_CONFIRMATION = 4;
+}
+
+// The immediate, async response after requesting a command execution.
+message ExecuteSlashCommandResponse {
+  // A unique taskID for this specific command execution.
+  string execution_id = 1;
+  // The initial status of the command execution.
+  CommandExecutionStatus status = 2;
+  // An optional message, particularly useful for explaining why a command
+  // failed to start.
+  string message = 3;
+}
+```
+
+## 4. Separation of Concerns
+
+We believe that all client-side context (ex., workspace state) and client-side tool execution (ex. read active buffers) should be routed through MCP.
+
+This approach enforces a strict separation of concerns: the A2A `development-tool` extension standardizes communication to the agent, while MCP serves as the single, authoritative interface for client-side capabilities.
+
+## Appendix
+
+### A. Example Interaction Flow
+
+1.  **Client -> Server**: The client sends a `message/stream` request containing the initial prompt and configuration in an `AgentSettings` object.
+2.  **Server -> Client**: SSE stream begins.
+    - **Event 1**: The server sends a `Task` object with `status.state: 'submitted'` and the new `taskId`.
+    - **Event 2**: The server sends a `TaskStatusUpdateEvent` with the metadata `kind` set to `'STATE_CHANGE'` and `status.state` set to `'working'`.
+3.  **Agent Logic**: The agent processes the prompt and decides to call the `write_file` tool, which requires user confirmation.
+4.  **Server -> Client**:
+    - **Event 3**: The server sends a `TaskStatusUpdateEvent`. The metadata `kind` is `'TOOL_CALL_UPDATE'`, and the `DataPart` contains a `ToolCall` object with its `status` as `'PENDING'` and a populated `confirmation_request`.
+    - **Event 4**: The server sends a final `TaskStatusUpdateEvent` for this exchange. The metadata `kind` is `'STATE_CHANGE'`, the `status.state` is `'input-required'`, and `final` is `true`. The stream for this request ends.
+5.  **Client**: The client UI renders the confirmation prompt based on the `ToolCall` object from Event 3. The user clicks "Approve."
+6.  **Client -> Server**: The client sends a new `message/stream` request. It includes the `taskId` from the ongoing task and a `DataPart` containing a `ToolCallConfirmation` object (e.g., `{"tool_call_id": "...", "selected_option_id": "proceed_once"}`).
+7.  **Server -> Client**: A new SSE stream begins for the second request.
+    - **Event 1**: The server sends a `TaskStatusUpdateEvent` with `kind: 'TOOL_CALL_UPDATE'`, containing the `ToolCall` object with its `status` now set to `'EXECUTING'`.
+    - **Event 2**: After the tool runs, the server sends another `TaskStatusUpdateEvent` with `kind: 'TOOL_CALL_UPDATE'`, containing the `ToolCall` with its `status` as `'SUCCEEDED'`.
+8.  **Agent Logic**: The agent receives the successful tool result and generates a final textual response.
+9.  **Server -> Client**:
+    - **Event 3**: The server sends a `TaskStatusUpdateEvent` with `kind: 'TEXT_CONTENT'` and a `TextPart` containing the agent's final answer.
+    - **Event 4**: The server sends the final `TaskStatusUpdateEvent`. The `kind` is `'STATE_CHANGE'`, the `status.state` is `'completed'`, and `final` is `true`. The stream ends.
+10. **Client**: The client displays the final answer. The task is now complete but can be continued by sending another message with the same `taskId`.

packages/a2a-server/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@google/gemini-cli-a2a-server",
-  "version": "0.3.2",
+  "version": "0.5.3",
   "private": true,
   "description": "Gemini CLI A2A Server",
   "repository": {
@@ -11,7 +11,7 @@
   "type": "module",
   "main": "dist/server.js",
   "scripts": {
-    "start": "node dist/src/server.js",
+    "start": "node dist/src/http/server.js",
     "build": "node ../../scripts/build_package.js",
     "lint": "eslint . --ext .ts,.tsx",
     "format": "prettier --write .",

packages/a2a-server/src/agent/executor.ts

@@ -4,10 +4,7 @@
  * SPDX-License-Identifier: Apache-2.0
  */
 
-import express from 'express';
-import { AsyncLocalStorage } from 'node:async_hooks';
-
-import type { Message, Task as SDKTask, AgentCard } from '@a2a-js/sdk';
+import type { Message, Task as SDKTask } from '@a2a-js/sdk';
 import type {
   TaskStore,
   AgentExecutor,
@@ -15,8 +12,6 @@ import type {
   RequestContext,
   ExecutionEventBus,
 } from '@a2a-js/sdk/server';
-import { DefaultRequestHandler, InMemoryTaskStore } from '@a2a-js/sdk/server';
-import { A2AExpressApp } from '@a2a-js/sdk/server/express'; // Import server components
 import type {
   ToolCallRequestInfo,
   ServerGeminiToolCallRequestEvent,
@@ -24,18 +19,23 @@ import type {
 } from '@google/gemini-cli-core';
 import { GeminiEventType } from '@google/gemini-cli-core';
 import { v4 as uuidv4 } from 'uuid';
-import { logger } from './logger.js';
-import type { StateChange, AgentSettings } from './types.js';
-import { CoderAgentEvent } from './types.js';
-import { loadConfig, loadEnvironment, setTargetDir } from './config.js';
-import { loadSettings } from './settings.js';
-import { loadExtensions } from './extension.js';
-import { Task } from './task.js';
-import { GCSTaskStore, NoOpTaskStore } from './gcs.js';
-import type { PersistedStateMetadata } from './metadata_types.js';
-import { getPersistedState, setPersistedState } from './metadata_types.js';
 
-const requestStorage = new AsyncLocalStorage<{ req: express.Request }>();
+import { logger } from '../utils/logger.js';
+import type {
+  StateChange,
+  AgentSettings,
+  PersistedStateMetadata,
+} from '../types.js';
+import {
+  CoderAgentEvent,
+  getPersistedState,
+  setPersistedState,
+} from '../types.js';
+import { loadConfig, loadEnvironment, setTargetDir } from '../config/config.js';
+import { loadSettings } from '../config/settings.js';
+import { loadExtensions } from '../config/extension.js';
+import { Task } from './task.js';
+import { requestStorage } from '../http/requestStorage.js';
 
 /**
  * Provides a wrapper for Task. Passes data from Task to SDKTask.
@@ -77,48 +77,10 @@ class TaskWrapper {
   }
 }
 
-const coderAgentCard: AgentCard = {
-  name: 'Gemini SDLC Agent',
-  description:
-    'An agent that generates code based on natural language instructions and streams file outputs.',
-  url: 'http://localhost:41242/',
-  provider: {
-    organization: 'Google',
-    url: 'https://google.com',
-  },
-  protocolVersion: '0.3.0',
-  version: '0.0.2', // Incremented version
-  capabilities: {
-    streaming: true,
-    pushNotifications: false,
-    stateTransitionHistory: true,
-  },
-  securitySchemes: undefined,
-  security: undefined,
-  defaultInputModes: ['text'],
-  defaultOutputModes: ['text'],
-  skills: [
-    {
-      id: 'code_generation',
-      name: 'Code Generation',
-      description:
-        'Generates code snippets or complete files based on user requests, streaming the results.',
-      tags: ['code', 'development', 'programming'],
-      examples: [
-        'Write a python function to calculate fibonacci numbers.',
-        'Create an HTML file with a basic button that alerts "Hello!" when clicked.',
-      ],
-      inputModes: ['text'],
-      outputModes: ['text'],
-    },
-  ],
-  supportsAuthenticatedExtendedCard: false,
-};
-
 /**
  * CoderAgentExecutor implements the agent's core logic for code generation.
  */
-class CoderAgentExecutor implements AgentExecutor {
+export class CoderAgentExecutor implements AgentExecutor {
   private tasks: Map<string, TaskWrapper> = new Map();
   // Track tasks with an active execution loop.
   private executingTasks = new Set<string>();
@@ -163,9 +125,7 @@ class CoderAgentExecutor implements AgentExecutor {
       eventBus,
     );
     runtimeTask.taskState = persistedState._taskState;
-    await runtimeTask.geminiClient.initialize(
-      runtimeTask.config.getContentGeneratorConfig(),
-    );
+    await runtimeTask.geminiClient.initialize();
 
     const wrapper = new TaskWrapper(runtimeTask, agentSettings);
     this.tasks.set(sdkTask.id, wrapper);
@@ -182,9 +142,7 @@ class CoderAgentExecutor implements AgentExecutor {
     const agentSettings = agentSettingsInput || ({} as AgentSettings);
     const config = await this.getConfig(agentSettings, taskId);
     const runtimeTask = await Task.create(taskId, contextId, config, eventBus);
-    await runtimeTask.geminiClient.initialize(
-      runtimeTask.config.getContentGeneratorConfig(),
-    );
+    await runtimeTask.geminiClient.initialize();
 
     const wrapper = new TaskWrapper(runtimeTask, agentSettings);
     this.tasks.set(taskId, wrapper);
@@ -639,147 +597,3 @@ class CoderAgentExecutor implements AgentExecutor {
     }
   }
 }
-
-export function updateCoderAgentCardUrl(port: number) {
-  coderAgentCard.url = `http://localhost:${port}/`;
-}
-
-export async function main() {
-  try {
-    const expressApp = await createApp();
-    const port = process.env['CODER_AGENT_PORT'] || 0;
-
-    const server = expressApp.listen(port, () => {
-      const address = server.address();
-      let actualPort;
-      if (process.env['CODER_AGENT_PORT']) {
-        actualPort = process.env['CODER_AGENT_PORT'];
-      } else if (address && typeof address !== 'string') {
-        actualPort = address.port;
-      } else {
-        throw new Error('[Core Agent] Could not find port number.');
-      }
-      updateCoderAgentCardUrl(Number(actualPort));
-      logger.info(
-        `[CoreAgent] Agent Server started on http://localhost:${actualPort}`,
-      );
-      logger.info(
-        `[CoreAgent] Agent Card: http://localhost:${actualPort}/.well-known/agent-card.json`,
-      );
-      logger.info('[CoreAgent] Press Ctrl+C to stop the server');
-    });
-  } catch (error) {
-    logger.error('[CoreAgent] Error during startup:', error);
-    process.exit(1);
-  }
-}
-
-export async function createApp() {
-  try {
-    // loadEnvironment() is called within getConfig now
-    const bucketName = process.env['GCS_BUCKET_NAME'];
-    let taskStoreForExecutor: TaskStore;
-    let taskStoreForHandler: TaskStore;
-
-    if (bucketName) {
-      logger.info(`Using GCSTaskStore with bucket: ${bucketName}`);
-      const gcsTaskStore = new GCSTaskStore(bucketName);
-      taskStoreForExecutor = gcsTaskStore;
-      taskStoreForHandler = new NoOpTaskStore(gcsTaskStore);
-    } else {
-      logger.info('Using InMemoryTaskStore');
-      const inMemoryTaskStore = new InMemoryTaskStore();
-      taskStoreForExecutor = inMemoryTaskStore;
-      taskStoreForHandler = inMemoryTaskStore;
-    }
-
-    const agentExecutor = new CoderAgentExecutor(taskStoreForExecutor);
-
-    const requestHandler = new DefaultRequestHandler(
-      coderAgentCard,
-      taskStoreForHandler,
-      agentExecutor,
-    );
-
-    let expressApp = express();
-    expressApp.use((req, res, next) => {
-      requestStorage.run({ req }, next);
-    });
-
-    const appBuilder = new A2AExpressApp(requestHandler);
-    expressApp = appBuilder.setupRoutes(expressApp, '');
-    expressApp.use(express.json());
-
-    expressApp.post('/tasks', async (req, res) => {
-      try {
-        const taskId = uuidv4();
-        const agentSettings = req.body.agentSettings as
-          | AgentSettings
-          | undefined;
-        const contextId = req.body.contextId || uuidv4();
-        const wrapper = await agentExecutor.createTask(
-          taskId,
-          contextId,
-          agentSettings,
-        );
-        await taskStoreForExecutor.save(wrapper.toSDKTask());
-        res.status(201).json(wrapper.id);
-      } catch (error) {
-        logger.error('[CoreAgent] Error creating task:', error);
-        const errorMessage =
-          error instanceof Error
-            ? error.message
-            : 'Unknown error creating task';
-        res.status(500).send({ error: errorMessage });
-      }
-    });
-
-    expressApp.get('/tasks/metadata', async (req, res) => {
-      // This endpoint is only meaningful if the task store is in-memory.
-      if (!(taskStoreForExecutor instanceof InMemoryTaskStore)) {
-        res.status(501).send({
-          error:
-            'Listing all task metadata is only supported when using InMemoryTaskStore.',
-        });
-      }
-      try {
-        const wrappers = agentExecutor.getAllTasks();
-        if (wrappers && wrappers.length > 0) {
-          const tasksMetadata = await Promise.all(
-            wrappers.map((wrapper) => wrapper.task.getMetadata()),
-          );
-          res.status(200).json(tasksMetadata);
-        } else {
-          res.status(204).send();
-        }
-      } catch (error) {
-        logger.error('[CoreAgent] Error getting all task metadata:', error);
-        const errorMessage =
-          error instanceof Error
-            ? error.message
-            : 'Unknown error getting task metadata';
-        res.status(500).send({ error: errorMessage });
-      }
-    });
-
-    expressApp.get('/tasks/:taskId/metadata', async (req, res) => {
-      const taskId = req.params.taskId;
-      let wrapper = agentExecutor.getTask(taskId);
-      if (!wrapper) {
-        const sdkTask = await taskStoreForExecutor.load(taskId);
-        if (sdkTask) {
-          wrapper = await agentExecutor.reconstruct(sdkTask);
-        }
-      }
-      if (!wrapper) {
-        res.status(404).send({ error: 'Task not found' });
-        return;
-      }
-      res.json({ metadata: await wrapper.task.getMetadata() });
-    });
-    return expressApp;
-  } catch (error) {
-    logger.error('[CoreAgent] Error during startup:', error);
-    process.exit(1);
-  }
-}

packages/a2a-server/src/agent/task.test.ts

@@ -0,0 +1,59 @@
+/**
+ * @license
+ * Copyright 2025 Google LLC
+ * SPDX-License-Identifier: Apache-2.0
+ */
+
+import { describe, it, expect, vi } from 'vitest';
+import { Task } from './task.js';
+import type { Config, ToolCallRequestInfo } from '@google/gemini-cli-core';
+import { createMockConfig } from '../utils/testing_utils.js';
+import type { ExecutionEventBus } from '@a2a-js/sdk/server';
+
+describe('Task', () => {
+  it('scheduleToolCalls should not modify the input requests array', async () => {
+    const mockConfig = createMockConfig();
+
+    const mockEventBus: ExecutionEventBus = {
+      publish: vi.fn(),
+      on: vi.fn(),
+      off: vi.fn(),
+      once: vi.fn(),
+      removeAllListeners: vi.fn(),
+      finished: vi.fn(),
+    };
+
+    // The Task constructor is private. We'll bypass it for this unit test.
+    // @ts-expect-error - Calling private constructor for test purposes.
+    const task = new Task(
+      'task-id',
+      'context-id',
+      mockConfig as Config,
+      mockEventBus,
+    );
+
+    task['setTaskStateAndPublishUpdate'] = vi.fn();
+    task['getProposedContent'] = vi.fn().mockResolvedValue('new content');
+
+    const requests: ToolCallRequestInfo[] = [
+      {
+        callId: '1',
+        name: 'replace',
+        args: {
+          file_path: 'test.txt',
+          old_string: 'old',
+          new_string: 'new',
+        },
+        isClientInitiated: false,
+        prompt_id: 'prompt-id-1',
+      },
+    ];
+
+    const originalRequests = JSON.parse(JSON.stringify(requests));
+    const abortController = new AbortController();
+
+    await task.scheduleToolCalls(requests, abortController.signal);
+
+    expect(requests).toEqual(originalRequests);
+  });
+});

packages/a2a-server/src/agent/task.ts

@@ -6,7 +6,7 @@
 
 import {
   CoreToolScheduler,
-  GeminiClient,
+  type GeminiClient,
   GeminiEventType,
   ToolConfirmationOutcome,
   ApprovalMode,
@@ -37,10 +37,10 @@ import type {
   Artifact,
 } from '@a2a-js/sdk';
 import { v4 as uuidv4 } from 'uuid';
-import { logger } from './logger.js';
+import { logger } from '../utils/logger.js';
 import * as fs from 'node:fs';
 
-import { CoderAgentEvent } from './types.js';
+import { CoderAgentEvent } from '../types.js';
 import type {
   CoderAgentMessage,
   StateChange,
@@ -49,7 +49,7 @@ import type {
   TaskMetadata,
   Thought,
   ThoughtSummary,
-} from './types.js';
+} from '../types.js';
 import type { PartUnion, Part as genAiPart } from '@google/genai';
 
 export class Task {
@@ -82,18 +82,17 @@ export class Task {
     this.contextId = contextId;
     this.config = config;
     this.scheduler = this.createScheduler();
-    this.geminiClient = new GeminiClient(this.config);
+    this.geminiClient = this.config.getGeminiClient();
     this.pendingToolConfirmationDetails = new Map();
     this.taskState = 'submitted';
     this.eventBus = eventBus;
     this.completedToolCalls = [];
     this._resetToolCompletionPromise();
-    this.config.setFlashFallbackHandler(
-      async (currentModel: string, fallbackModel: string): Promise<boolean> => {
-        config.setModel(fallbackModel); // gemini-cli-core sets to DEFAULT_GEMINI_FLASH_MODEL
-        // Switch model for future use but return false to stop current retry
-        return false;
-      },
+    this.config.setFallbackModelHandler(
+      // For a2a-server, we want to automatically switch to the fallback model
+      // for future requests without retrying the current one. The 'stop'
+      // intent achieves this.
+      async () => 'stop',
     );
   }
 
@@ -227,7 +226,7 @@ export class Task {
     } = {
       coderAgent: coderAgentMessage,
       model: this.config.getModel(),
-      userTier: this.geminiClient.getUserTier(),
+      userTier: this.config.getUserTier(),
     };
 
     if (metadataError) {
@@ -520,30 +519,36 @@ export class Task {
       return;
     }
 
-    for (const request of requests) {
-      if (
-        !request.args['newContent'] &&
-        request.name === 'replace' &&
-        request.args &&
-        request.args['file_path'] &&
-        request.args['old_string'] &&
-        request.args['new_string']
-      ) {
-        request.args['newContent'] = await this.getProposedContent(
-          request.args['file_path'] as string,
-          request.args['old_string'] as string,
-          request.args['new_string'] as string,
-        );
-      }
-    }
+    const updatedRequests = await Promise.all(
+      requests.map(async (request) => {
+        if (
+          request.name === 'replace' &&
+          request.args &&
+          !request.args['newContent'] &&
+          request.args['file_path'] &&
+          request.args['old_string'] &&
+          request.args['new_string']
+        ) {
+          const newContent = await this.getProposedContent(
+            request.args['file_path'] as string,
+            request.args['old_string'] as string,
+            request.args['new_string'] as string,
+          );
+          return { ...request, args: { ...request.args, newContent } };
+        }
+        return request;
+      }),
+    );
 
-    logger.info(`[Task] Scheduling batch of ${requests.length} tool calls.`);
+    logger.info(
+      `[Task] Scheduling batch of ${updatedRequests.length} tool calls.`,
+    );
     const stateChange: StateChange = {
       kind: CoderAgentEvent.StateChangeEvent,
     };
     this.setTaskStateAndPublishUpdate('working', stateChange);
 
-    await this.scheduler.schedule(requests, abortSignal);
+    await this.scheduler.schedule(updatedRequests, abortSignal);
   }
 
   async acceptAgentMessage(event: ServerGeminiStreamEvent): Promise<void> {

packages/a2a-server/src/config/config.ts

@@ -22,10 +22,10 @@ import {
   DEFAULT_GEMINI_MODEL,
 } from '@google/gemini-cli-core';
 
-import { logger } from './logger.js';
+import { logger } from '../utils/logger.js';
 import type { Settings } from './settings.js';
 import type { Extension } from './extension.js';
-import { type AgentSettings, CoderAgentEvent } from './types.js';
+import { type AgentSettings, CoderAgentEvent } from '../types.js';
 
 export async function loadConfig(
   settings: Settings,
@@ -79,10 +79,10 @@ export async function loadConfig(
     false,
     fileService,
     extensionContextFilePaths,
+    true, /// TODO: Wire up folder trust logic here.
   );
   configParams.userMemory = memoryContent;
   configParams.geminiMdFileCount = fileCount;
-
   const config = new Config({
     ...configParams,
   });

packages/a2a-server/src/config/extension.ts

@@ -10,7 +10,7 @@ import type { MCPServerConfig } from '@google/gemini-cli-core';
 import * as fs from 'node:fs';
 import * as path from 'node:path';
 import * as os from 'node:os';
-import { logger } from './logger.js';
+import { logger } from '../utils/logger.js';
 
 export const EXTENSIONS_DIRECTORY_NAME = path.join('.gemini', 'extensions');
 export const EXTENSIONS_CONFIG_FILENAME = 'gemini-extension.json';

packages/a2a-server/src/http/app.test.ts

@@ -27,13 +27,14 @@ import {
   it,
   vi,
 } from 'vitest';
-import { createApp } from './agent.js';
+import { createApp } from './app.js';
 import {
   assertUniqueFinalEventIsLast,
   assertTaskCreationAndWorkingStatus,
   createStreamMessageRequest,
-  MockTool,
-} from './testing_utils.js';
+  createMockConfig,
+} from '../utils/testing_utils.js';
+import { MockTool } from '@google/gemini-cli-core';
 
 const mockToolConfirmationFn = async () =>
   ({}) as unknown as ToolCallConfirmationDetails;
@@ -56,38 +57,23 @@ const streamToSSEEvents = (
 
 // Mock the logger to avoid polluting test output
 // Comment out to debug tests
-vi.mock('./logger.js', () => ({
+vi.mock('../utils/logger.js', () => ({
   logger: { info: vi.fn(), warn: vi.fn(), error: vi.fn() },
 }));
 
 let config: Config;
 const getToolRegistrySpy = vi.fn().mockReturnValue(ApprovalMode.DEFAULT);
 const getApprovalModeSpy = vi.fn();
-vi.mock('./config.js', async () => {
-  const actual = await vi.importActual('./config.js');
+vi.mock('../config/config.js', async () => {
+  const actual = await vi.importActual('../config/config.js');
   return {
     ...actual,
     loadConfig: vi.fn().mockImplementation(async () => {
-      config = {
+      const mockConfig = createMockConfig({
         getToolRegistry: getToolRegistrySpy,
         getApprovalMode: getApprovalModeSpy,
-        getIdeMode: vi.fn().mockReturnValue(false),
-        getAllowedTools: vi.fn().mockReturnValue([]),
-        getIdeClient: vi.fn(),
-        getWorkspaceContext: vi.fn().mockReturnValue({
-          isPathWithinWorkspace: () => true,
-        }),
-        getTargetDir: () => '/test',
-        getGeminiClient: vi.fn(),
-        getDebugMode: vi.fn().mockReturnValue(false),
-        getContentGeneratorConfig: vi
-          .fn()
-          .mockReturnValue({ model: 'gemini-pro' }),
-        getModel: vi.fn().mockReturnValue('gemini-pro'),
-        getUsageStatisticsEnabled: vi.fn().mockReturnValue(false),
-        setFlashFallbackHandler: vi.fn(),
-        initialize: vi.fn().mockResolvedValue(undefined),
-      } as unknown as Config;
+      });
+      config = mockConfig as Config;
       return config;
     }),
   };
@@ -189,13 +175,10 @@ describe('E2E Tests', () => {
       yield* [];
     });
 
-    const mockTool = new MockTool(
-      'test-tool',
-      'Test Tool',
-      true,
-      false,
-      mockToolConfirmationFn,
-    );
+    const mockTool = new MockTool({
+      name: 'test-tool',
+      shouldConfirmExecute: vi.fn(mockToolConfirmationFn),
+    });
 
     getToolRegistrySpy.mockReturnValue({
       getAllTools: vi.fn().mockReturnValue([mockTool]),
@@ -284,20 +267,16 @@ describe('E2E Tests', () => {
       yield* [];
     });
 
-    const mockTool1 = new MockTool(
-      'test-tool-1',
-      'Test Tool 1',
-      false,
-      false,
-      mockToolConfirmationFn,
-    );
-    const mockTool2 = new MockTool(
-      'test-tool-2',
-      'Test Tool 2',
-      false,
-      false,
-      mockToolConfirmationFn,
-    );
+    const mockTool1 = new MockTool({
+      name: 'test-tool-1',
+      displayName: 'Test Tool 1',
+      shouldConfirmExecute: vi.fn(mockToolConfirmationFn),
+    });
+    const mockTool2 = new MockTool({
+      name: 'test-tool-2',
+      displayName: 'Test Tool 2',
+      shouldConfirmExecute: vi.fn(mockToolConfirmationFn),
+    });
 
     getToolRegistrySpy.mockReturnValue({
       getAllTools: vi.fn().mockReturnValue([mockTool1, mockTool2]),
@@ -404,13 +383,13 @@ describe('E2E Tests', () => {
       yield* [{ type: 'content', value: 'Tool executed successfully.' }];
     });
 
-    const mockTool = new MockTool(
-      'test-tool-no-approval',
-      'Test Tool No Approval',
-    );
-    mockTool.execute.mockResolvedValue({
-      llmContent: 'Tool executed successfully.',
-      returnDisplay: 'Tool executed successfully.',
+    const mockTool = new MockTool({
+      name: 'test-tool-no-approval',
+      displayName: 'Test Tool No Approval',
+      execute: vi.fn().mockResolvedValue({
+        llmContent: 'Tool executed successfully.',
+        returnDisplay: 'Tool executed successfully.',
+      }),
     });
 
     getToolRegistrySpy.mockReturnValue({
@@ -535,15 +514,13 @@ describe('E2E Tests', () => {
     // Set approval mode to yolo
     getApprovalModeSpy.mockReturnValue(ApprovalMode.YOLO);
 
-    const mockTool = new MockTool(
-      'test-tool-yolo',
-      'Test Tool YOLO',
-      false,
-      false,
-    );
-    mockTool.execute.mockResolvedValue({
-      llmContent: 'Tool executed successfully.',
-      returnDisplay: 'Tool executed successfully.',
+    const mockTool = new MockTool({
+      name: 'test-tool-yolo',
+      displayName: 'Test Tool YOLO',
+      execute: vi.fn().mockResolvedValue({
+        llmContent: 'Tool executed successfully.',
+        returnDisplay: 'Tool executed successfully.',
+      }),
     });
 
     getToolRegistrySpy.mockReturnValue({

packages/a2a-server/src/http/app.ts

@@ -0,0 +1,200 @@
+/**
+ * @license
+ * Copyright 2025 Google LLC
+ * SPDX-License-Identifier: Apache-2.0
+ */
+
+import express from 'express';
+
+import type { AgentCard } from '@a2a-js/sdk';
+import type { TaskStore } from '@a2a-js/sdk/server';
+import { DefaultRequestHandler, InMemoryTaskStore } from '@a2a-js/sdk/server';
+import { A2AExpressApp } from '@a2a-js/sdk/server/express'; // Import server components
+import { v4 as uuidv4 } from 'uuid';
+import { logger } from '../utils/logger.js';
+import type { AgentSettings } from '../types.js';
+import { GCSTaskStore, NoOpTaskStore } from '../persistence/gcs.js';
+import { CoderAgentExecutor } from '../agent/executor.js';
+import { requestStorage } from './requestStorage.js';
+
+const coderAgentCard: AgentCard = {
+  name: 'Gemini SDLC Agent',
+  description:
+    'An agent that generates code based on natural language instructions and streams file outputs.',
+  url: 'http://localhost:41242/',
+  provider: {
+    organization: 'Google',
+    url: 'https://google.com',
+  },
+  protocolVersion: '0.3.0',
+  version: '0.0.2', // Incremented version
+  capabilities: {
+    streaming: true,
+    pushNotifications: false,
+    stateTransitionHistory: true,
+  },
+  securitySchemes: undefined,
+  security: undefined,
+  defaultInputModes: ['text'],
+  defaultOutputModes: ['text'],
+  skills: [
+    {
+      id: 'code_generation',
+      name: 'Code Generation',
+      description:
+        'Generates code snippets or complete files based on user requests, streaming the results.',
+      tags: ['code', 'development', 'programming'],
+      examples: [
+        'Write a python function to calculate fibonacci numbers.',
+        'Create an HTML file with a basic button that alerts "Hello!" when clicked.',
+      ],
+      inputModes: ['text'],
+      outputModes: ['text'],
+    },
+  ],
+  supportsAuthenticatedExtendedCard: false,
+};
+
+export function updateCoderAgentCardUrl(port: number) {
+  coderAgentCard.url = `http://localhost:${port}/`;
+}
+
+export async function createApp() {
+  try {
+    // loadEnvironment() is called within getConfig now
+    const bucketName = process.env['GCS_BUCKET_NAME'];
+    let taskStoreForExecutor: TaskStore;
+    let taskStoreForHandler: TaskStore;
+
+    if (bucketName) {
+      logger.info(`Using GCSTaskStore with bucket: ${bucketName}`);
+      const gcsTaskStore = new GCSTaskStore(bucketName);
+      taskStoreForExecutor = gcsTaskStore;
+      taskStoreForHandler = new NoOpTaskStore(gcsTaskStore);
+    } else {
+      logger.info('Using InMemoryTaskStore');
+      const inMemoryTaskStore = new InMemoryTaskStore();
+      taskStoreForExecutor = inMemoryTaskStore;
+      taskStoreForHandler = inMemoryTaskStore;
+    }
+
+    const agentExecutor = new CoderAgentExecutor(taskStoreForExecutor);
+
+    const requestHandler = new DefaultRequestHandler(
+      coderAgentCard,
+      taskStoreForHandler,
+      agentExecutor,
+    );
+
+    let expressApp = express();
+    expressApp.use((req, res, next) => {
+      requestStorage.run({ req }, next);
+    });
+
+    const appBuilder = new A2AExpressApp(requestHandler);
+    expressApp = appBuilder.setupRoutes(expressApp, '');
+    expressApp.use(express.json());
+
+    expressApp.post('/tasks', async (req, res) => {
+      try {
+        const taskId = uuidv4();
+        const agentSettings = req.body.agentSettings as
+          | AgentSettings
+          | undefined;
+        const contextId = req.body.contextId || uuidv4();
+        const wrapper = await agentExecutor.createTask(
+          taskId,
+          contextId,
+          agentSettings,
+        );
+        await taskStoreForExecutor.save(wrapper.toSDKTask());
+        res.status(201).json(wrapper.id);
+      } catch (error) {
+        logger.error('[CoreAgent] Error creating task:', error);
+        const errorMessage =
+          error instanceof Error
+            ? error.message
+            : 'Unknown error creating task';
+        res.status(500).send({ error: errorMessage });
+      }
+    });
+
+    expressApp.get('/tasks/metadata', async (req, res) => {
+      // This endpoint is only meaningful if the task store is in-memory.
+      if (!(taskStoreForExecutor instanceof InMemoryTaskStore)) {
+        res.status(501).send({
+          error:
+            'Listing all task metadata is only supported when using InMemoryTaskStore.',
+        });
+      }
+      try {
+        const wrappers = agentExecutor.getAllTasks();
+        if (wrappers && wrappers.length > 0) {
+          const tasksMetadata = await Promise.all(
+            wrappers.map((wrapper) => wrapper.task.getMetadata()),
+          );
+          res.status(200).json(tasksMetadata);
+        } else {
+          res.status(204).send();
+        }
+      } catch (error) {
+        logger.error('[CoreAgent] Error getting all task metadata:', error);
+        const errorMessage =
+          error instanceof Error
+            ? error.message
+            : 'Unknown error getting task metadata';
+        res.status(500).send({ error: errorMessage });
+      }
+    });
+
+    expressApp.get('/tasks/:taskId/metadata', async (req, res) => {
+      const taskId = req.params.taskId;
+      let wrapper = agentExecutor.getTask(taskId);
+      if (!wrapper) {
+        const sdkTask = await taskStoreForExecutor.load(taskId);
+        if (sdkTask) {
+          wrapper = await agentExecutor.reconstruct(sdkTask);
+        }
+      }
+      if (!wrapper) {
+        res.status(404).send({ error: 'Task not found' });
+        return;
+      }
+      res.json({ metadata: await wrapper.task.getMetadata() });
+    });
+    return expressApp;
+  } catch (error) {
+    logger.error('[CoreAgent] Error during startup:', error);
+    process.exit(1);
+  }
+}
+
+export async function main() {
+  try {
+    const expressApp = await createApp();
+    const port = process.env['CODER_AGENT_PORT'] || 0;
+
+    const server = expressApp.listen(port, () => {
+      const address = server.address();
+      let actualPort;
+      if (process.env['CODER_AGENT_PORT']) {
+        actualPort = process.env['CODER_AGENT_PORT'];
+      } else if (address && typeof address !== 'string') {
+        actualPort = address.port;
+      } else {
+        throw new Error('[Core Agent] Could not find port number.');
+      }
+      updateCoderAgentCardUrl(Number(actualPort));
+      logger.info(
+        `[CoreAgent] Agent Server started on http://localhost:${actualPort}`,
+      );
+      logger.info(
+        `[CoreAgent] Agent Card: http://localhost:${actualPort}/.well-known/agent-card.json`,
+      );
+      logger.info('[CoreAgent] Press Ctrl+C to stop the server');
+    });
+  } catch (error) {
+    logger.error('[CoreAgent] Error during startup:', error);
+    process.exit(1);
+  }
+}

packages/a2a-server/src/http/endpoints.test.ts

@@ -7,22 +7,22 @@
 import { describe, it, expect, beforeAll, afterAll, vi } from 'vitest';
 import request from 'supertest';
 import type express from 'express';
-import { createApp, updateCoderAgentCardUrl } from './agent.js';
+import { createApp, updateCoderAgentCardUrl } from './app.js';
 import * as fs from 'node:fs';
 import * as path from 'node:path';
 import * as os from 'node:os';
 import type { Server } from 'node:http';
-import type { TaskMetadata } from './types.js';
+import type { TaskMetadata } from '../types.js';
 import type { AddressInfo } from 'node:net';
 
 // Mock the logger to avoid polluting test output
 // Comment out to help debug
-vi.mock('./logger.js', () => ({
+vi.mock('../utils/logger.js', () => ({
   logger: { info: vi.fn(), warn: vi.fn(), error: vi.fn() },
 }));
 
 // Mock Task.create to avoid its complex setup
-vi.mock('./task.js', () => {
+vi.mock('../agent/task.js', () => {
   class MockTask {
     id: string;
     contextId: string;
@@ -88,21 +88,24 @@ describe('Agent Server Endpoints', () => {
     });
   });
 
-  afterAll(
-    () =>
-      new Promise<void>((resolve, reject) => {
+  afterAll(async () => {
+    if (server) {
+      await new Promise<void>((resolve, reject) => {
         server.close((err) => {
           if (err) return reject(err);
-
-          try {
-            fs.rmSync(testWorkspace, { recursive: true, force: true });
-          } catch (e) {
-            console.warn(`Could not remove temp dir '${testWorkspace}':`, e);
-          }
           resolve();
         });
-      }),
-  );
+      });
+    }
+
+    if (testWorkspace) {
+      try {
+        fs.rmSync(testWorkspace, { recursive: true, force: true });
+      } catch (e) {
+        console.warn(`Could not remove temp dir '${testWorkspace}':`, e);
+      }
+    }
+  });
 
   it('should create a new task via POST /tasks', async () => {
     const response = await createTask('test-context');

packages/a2a-server/src/http/requestStorage.ts

@@ -0,0 +1,10 @@
+/**
+ * @license
+ * Copyright 2025 Google LLC
+ * SPDX-License-Identifier: Apache-2.0
+ */
+
+import type express from 'express';
+import { AsyncLocalStorage } from 'node:async_hooks';
+
+export const requestStorage = new AsyncLocalStorage<{ req: express.Request }>();

packages/a2a-server/src/http/server.ts

@@ -7,8 +7,8 @@
 import * as url from 'node:url';
 import * as path from 'node:path';
 
-import { logger } from './logger.js';
-import { main } from './agent.js';
+import { logger } from '../utils/logger.js';
+import { main } from './app.js';
 
 // Check if the module is the main script being run. path.resolve() creates a
 // canonical, absolute path, which avoids cross-platform issues.

packages/a2a-server/src/index.ts

@@ -4,5 +4,6 @@
  * SPDX-License-Identifier: Apache-2.0
  */
 
-export * from './agent.js';
+export * from './agent/executor.js';
+export * from './http/app.js';
 export * from './types.js';

packages/a2a-server/src/metadata_types.ts

@@ -1,33 +0,0 @@
-/**
- * @license
- * Copyright 2025 Google LLC
- * SPDX-License-Identifier: Apache-2.0
- */
-
-import type { AgentSettings } from './types.js';
-import type { TaskState } from '@a2a-js/sdk';
-
-export interface PersistedStateMetadata {
-  _agentSettings: AgentSettings;
-  _taskState: TaskState;
-}
-
-export type PersistedTaskMetadata = { [k: string]: unknown };
-
-export const METADATA_KEY = '__persistedState';
-
-export function getPersistedState(
-  metadata: PersistedTaskMetadata,
-): PersistedStateMetadata | undefined {
-  return metadata?.[METADATA_KEY] as PersistedStateMetadata | undefined;
-}
-
-export function setPersistedState(
-  metadata: PersistedTaskMetadata,
-  state: PersistedStateMetadata,
-): PersistedTaskMetadata {
-  return {
-    ...metadata,
-    [METADATA_KEY]: state,
-  };
-}

packages/a2a-server/src/persistence/gcs.test.ts

@@ -16,9 +16,9 @@ import type { Mocked, MockedClass, Mock } from 'vitest';
 import { describe, it, expect, beforeEach, vi } from 'vitest';
 
 import { GCSTaskStore, NoOpTaskStore } from './gcs.js';
-import { logger } from './logger.js';
-import * as configModule from './config.js';
-import * as metadataModule from './metadata_types.js';
+import { logger } from '../utils/logger.js';
+import * as configModule from '../config/config.js';
+import { getPersistedState, METADATA_KEY } from '../types.js';
 
 // Mock dependencies
 vi.mock('@google-cloud/storage');
@@ -42,7 +42,7 @@ vi.mock('node:fs', async () => {
 vi.mock('tar');
 vi.mock('zlib');
 vi.mock('uuid');
-vi.mock('./logger', () => ({
+vi.mock('../utils/logger.js', () => ({
   logger: {
     info: vi.fn(),
     warn: vi.fn(),
@@ -50,11 +50,19 @@ vi.mock('./logger', () => ({
     debug: vi.fn(),
   },
 }));
-vi.mock('./config');
-vi.mock('./metadata_types');
+vi.mock('../config/config.js', () => ({
+  setTargetDir: vi.fn(),
+}));
 vi.mock('node:stream/promises', () => ({
   pipeline: vi.fn(),
 }));
+vi.mock('../types.js', async (importOriginal) => {
+  const actual = await importOriginal<typeof import('../types.js')>();
+  return {
+    ...actual,
+    getPersistedState: vi.fn(),
+  };
+});
 
 const mockStorage = Storage as MockedClass<typeof Storage>;
 const mockFse = fse as Mocked<typeof fse>;
@@ -64,8 +72,8 @@ const mockGzipSync = gzipSync as Mock;
 const mockGunzipSync = gunzipSync as Mock;
 const mockUuidv4 = uuidv4 as Mock;
 const mockSetTargetDir = configModule.setTargetDir as Mock;
-const mockGetPersistedState = metadataModule.getPersistedState as Mock;
-const METADATA_KEY = metadataModule.METADATA_KEY || '__persistedState';
+const mockGetPersistedState = getPersistedState as Mock;
+const TEST_METADATA_KEY = METADATA_KEY || '__persistedState';
 
 type MockWriteStream = {
   on: Mock<
@@ -226,7 +234,10 @@ describe('GCSTaskStore', () => {
       mockGunzipSync.mockReturnValue(
         Buffer.from(
           JSON.stringify({
-            [METADATA_KEY]: { _agentSettings: {}, _taskState: 'submitted' },
+            [TEST_METADATA_KEY]: {
+              _agentSettings: {},
+              _taskState: 'submitted',
+            },
             _contextId: 'ctx1',
           }),
         ),
@@ -280,7 +291,10 @@ describe('GCSTaskStore', () => {
       mockGunzipSync.mockReturnValue(
         Buffer.from(
           JSON.stringify({
-            [METADATA_KEY]: { _agentSettings: {}, _taskState: 'submitted' },
+            [TEST_METADATA_KEY]: {
+              _agentSettings: {},
+              _taskState: 'submitted',
+            },
             _contextId: 'ctx1',
           }),
         ),

packages/a2a-server/src/persistence/gcs.ts

@@ -13,12 +13,9 @@ import { tmpdir } from 'node:os';
 import { join } from 'node:path';
 import type { Task as SDKTask } from '@a2a-js/sdk';
 import type { TaskStore } from '@a2a-js/sdk/server';
-import { logger } from './logger.js';
-import { setTargetDir } from './config.js';
-import {
-  getPersistedState,
-  type PersistedTaskMetadata,
-} from './metadata_types.js';
+import { logger } from '../utils/logger.js';
+import { setTargetDir } from '../config/config.js';
+import { getPersistedState, type PersistedTaskMetadata } from '../types.js';
 import { v4 as uuidv4 } from 'uuid';
 
 type ObjectType = 'metadata' | 'workspace';

packages/a2a-server/src/types.ts

@@ -102,3 +102,28 @@ export interface TaskMetadata {
     parameterSchema: unknown;
   }>;
 }
+
+export interface PersistedStateMetadata {
+  _agentSettings: AgentSettings;
+  _taskState: TaskState;
+}
+
+export type PersistedTaskMetadata = { [k: string]: unknown };
+
+export const METADATA_KEY = '__persistedState';
+
+export function getPersistedState(
+  metadata: PersistedTaskMetadata,
+): PersistedStateMetadata | undefined {
+  return metadata?.[METADATA_KEY] as PersistedStateMetadata | undefined;
+}
+
+export function setPersistedState(
+  metadata: PersistedTaskMetadata,
+  state: PersistedStateMetadata,
+): PersistedTaskMetadata {
+  return {
+    ...metadata,
+    [METADATA_KEY]: state,
+  };
+}

packages/a2a-server/src/utils/testing_utils.ts

@@ -10,88 +10,53 @@ import type {
   SendStreamingMessageSuccessResponse,
 } from '@a2a-js/sdk';
 import {
-  BaseDeclarativeTool,
-  BaseToolInvocation,
-  Kind,
-} from '@google/gemini-cli-core';
-import type {
-  ToolCallConfirmationDetails,
-  ToolResult,
-  ToolInvocation,
+  ApprovalMode,
+  DEFAULT_TRUNCATE_TOOL_OUTPUT_LINES,
+  DEFAULT_TRUNCATE_TOOL_OUTPUT_THRESHOLD,
+  GeminiClient,
 } from '@google/gemini-cli-core';
+import type { Config, Storage } from '@google/gemini-cli-core';
 import { expect, vi } from 'vitest';
 
-export const mockOnUserConfirmForToolConfirmation = vi.fn();
+export function createMockConfig(
+  overrides: Partial<Config> = {},
+): Partial<Config> {
+  const mockConfig = {
+    getToolRegistry: vi.fn().mockReturnValue({
+      getTool: vi.fn(),
+      getAllToolNames: vi.fn().mockReturnValue([]),
+    }),
+    getApprovalMode: vi.fn().mockReturnValue(ApprovalMode.DEFAULT),
+    getIdeMode: vi.fn().mockReturnValue(false),
+    getAllowedTools: vi.fn().mockReturnValue([]),
+    getWorkspaceContext: vi.fn().mockReturnValue({
+      isPathWithinWorkspace: () => true,
+    }),
+    getTargetDir: () => '/test',
+    storage: {
+      getProjectTempDir: () => '/tmp',
+    } as Storage,
+    getTruncateToolOutputThreshold: () =>
+      DEFAULT_TRUNCATE_TOOL_OUTPUT_THRESHOLD,
+    getTruncateToolOutputLines: () => DEFAULT_TRUNCATE_TOOL_OUTPUT_LINES,
+    getDebugMode: vi.fn().mockReturnValue(false),
+    getContentGeneratorConfig: vi.fn().mockReturnValue({ model: 'gemini-pro' }),
+    getModel: vi.fn().mockReturnValue('gemini-pro'),
+    getUsageStatisticsEnabled: vi.fn().mockReturnValue(false),
+    setFallbackModelHandler: vi.fn(),
+    initialize: vi.fn().mockResolvedValue(undefined),
+    getProxy: vi.fn().mockReturnValue(undefined),
+    getHistory: vi.fn().mockReturnValue([]),
+    getEmbeddingModel: vi.fn().mockReturnValue('text-embedding-004'),
+    getSessionId: vi.fn().mockReturnValue('test-session-id'),
+    getUserTier: vi.fn(),
+    ...overrides,
+  } as unknown as Config;
 
-export class MockToolInvocation extends BaseToolInvocation<object, ToolResult> {
-  constructor(
-    private readonly tool: MockTool,
-    params: object,
-  ) {
-    super(params);
-  }
-
-  getDescription(): string {
-    return JSON.stringify(this.params);
-  }
-
-  override shouldConfirmExecute(
-    abortSignal: AbortSignal,
-  ): Promise<ToolCallConfirmationDetails | false> {
-    return this.tool.shouldConfirmExecute(this.params, abortSignal);
-  }
-
-  execute(
-    signal: AbortSignal,
-    updateOutput?: (output: string) => void,
-    terminalColumns?: number,
-    terminalRows?: number,
-  ): Promise<ToolResult> {
-    return this.tool.execute(
-      this.params,
-      signal,
-      updateOutput,
-      terminalColumns,
-      terminalRows,
-    );
-  }
-}
-
-// TODO: dedup with gemini-cli, add shouldConfirmExecute() support in core
-export class MockTool extends BaseDeclarativeTool<object, ToolResult> {
-  constructor(
-    name: string,
-    displayName: string,
-    canUpdateOutput = false,
-    isOutputMarkdown = false,
-    shouldConfirmExecute?: () => Promise<ToolCallConfirmationDetails | false>,
-  ) {
-    super(
-      name,
-      displayName,
-      'A mock tool for testing',
-      Kind.Other,
-      {},
-      isOutputMarkdown,
-      canUpdateOutput,
-    );
-
-    if (shouldConfirmExecute) {
-      this.shouldConfirmExecute.mockImplementation(shouldConfirmExecute);
-    } else {
-      // Default to no confirmation needed
-      this.shouldConfirmExecute.mockResolvedValue(false);
-    }
-  }
-
-  execute = vi.fn();
-  shouldConfirmExecute = vi.fn();
-
-  protected createInvocation(
-    params: object,
-  ): ToolInvocation<object, ToolResult> {
-    return new MockToolInvocation(this, params);
-  }
+  mockConfig.getGeminiClient = vi
+    .fn()
+    .mockReturnValue(new GeminiClient(mockConfig));
+  return mockConfig;
 }
 
 export function createStreamMessageRequest(

packages/cli/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@google/gemini-cli",
-  "version": "0.3.2",
+  "version": "0.5.3",
   "description": "Gemini CLI",
   "repository": {
     "type": "git",
@@ -25,11 +25,11 @@
     "dist"
   ],
   "config": {
-    "sandboxImageUri": "us-docker.pkg.dev/gemini-code-dev/gemini-cli/sandbox:0.3.2"
+    "sandboxImageUri": "us-docker.pkg.dev/gemini-code-dev/gemini-cli/sandbox:0.5.3"
   },
   "dependencies": {
     "@google/gemini-cli-core": "file:../core",
-    "@google/genai": "1.13.0",
+    "@google/genai": "1.16.0",
     "@iarna/toml": "^2.2.5",
     "@modelcontextprotocol/sdk": "^1.15.1",
     "@types/update-notifier": "^6.0.8",
@@ -42,9 +42,7 @@
     "ink": "^6.2.3",
     "ink-gradient": "^3.0.0",
     "ink-spinner": "^5.0.0",
-    "lodash-es": "^4.17.21",
     "lowlight": "^3.3.0",
-    "mime-types": "^3.0.1",
     "open": "^10.1.2",
     "react": "^19.1.0",
     "read-package-up": "^11.0.0",
@@ -65,7 +63,6 @@
     "@types/command-exists": "^1.2.3",
     "@types/diff": "^7.0.2",
     "@types/dotenv": "^6.1.1",
-    "@types/lodash-es": "^4.17.12",
     "@types/node": "^20.11.24",
     "@types/react": "^19.1.8",
     "@types/react-dom": "^19.1.6",

packages/cli/src/commands/extensions.tsx

@@ -11,6 +11,8 @@ import { listCommand } from './extensions/list.js';
 import { updateCommand } from './extensions/update.js';
 import { disableCommand } from './extensions/disable.js';
 import { enableCommand } from './extensions/enable.js';
+import { linkCommand } from './extensions/link.js';
+import { newCommand } from './extensions/new.js';
 
 export const extensionsCommand: CommandModule = {
   command: 'extensions <command>',
@@ -23,6 +25,8 @@ export const extensionsCommand: CommandModule = {
       .command(updateCommand)
       .command(disableCommand)
       .command(enableCommand)
+      .command(linkCommand)
+      .command(newCommand)
       .demandCommand(1, 'You need at least one command before continuing.')
       .version(false),
   handler: () => {

packages/cli/src/commands/extensions/enable.ts

@@ -35,7 +35,7 @@ export async function handleEnable(args: EnableArgs) {
 }
 
 export const enableCommand: CommandModule = {
-  command: 'disable [--scope] <name>',
+  command: 'enable [--scope] <name>',
   describe: 'Enables an extension.',
   builder: (yargs) =>
     yargs

packages/cli/src/commands/extensions/examples/context/GEMINI.md

@@ -0,0 +1,8 @@
+# Ink Library Screen Reader Guidance
+
+When building custom components, it's important to keep accessibility in mind. While Ink provides the building blocks, ensuring your components are accessible will make your CLIs usable by a wider audience.
+
+## General Principles
+
+Provide screen reader-friendly output: Use the useIsScreenReaderEnabled hook to detect if a screen reader is active. You can then render a more descriptive output for screen reader users.
+Leverage ARIA props: For components that have a specific role (e.g., a checkbox or a button), use the aria-role, aria-state, and aria-label props on <Box> and <Text> to provide semantic meaning to screen readers.

packages/cli/src/commands/extensions/examples/context/gemini-extension.json

@@ -0,0 +1,5 @@
+{
+  "name": "context-example",
+  "version": "1.0.0",
+  "contextFileName": "GEMINI.md"
+}

packages/cli/src/commands/extensions/examples/custom-commands/commands/fs/grep-code.toml

@@ -0,0 +1,6 @@
+prompt = """
+Please summarize the findings for the pattern `{{args}}`.
+
+Search Results:
+!{grep -r {{args}} .}
+"""

packages/cli/src/commands/extensions/examples/custom-commands/gemini-extension.json

@@ -0,0 +1,4 @@
+{
+  "name": "custom-commands",
+  "version": "1.0.0"
+}

packages/cli/src/commands/extensions/examples/exclude-tools/gemini-extension.json

@@ -0,0 +1,5 @@
+{
+  "name": "excludeTools",
+  "version": "1.0.0",
+  "excludeTools": ["run_shell_command(rm -rf)"]
+}

packages/cli/src/commands/extensions/examples/mcp-server/example.ts

@@ -0,0 +1,60 @@
+/**
+ * @license
+ * Copyright 2025 Google LLC
+ * SPDX-License-Identifier: Apache-2.0
+ */
+
+import { McpServer } from '@modelcontextprotocol/sdk/server/mcp.js';
+import { StdioServerTransport } from '@modelcontextprotocol/sdk/server/stdio.js';
+import { z } from 'zod';
+
+const server = new McpServer({
+  name: 'prompt-server',
+  version: '1.0.0',
+});
+
+server.registerTool(
+  'fetch_posts',
+  {
+    description: 'Fetches a list of posts from a public API.',
+    inputSchema: z.object({}).shape,
+  },
+  async () => {
+    const apiResponse = await fetch(
+      'https://jsonplaceholder.typicode.com/posts',
+    );
+    const posts = await apiResponse.json();
+    const response = { posts: posts.slice(0, 5) };
+    return {
+      content: [
+        {
+          type: 'text',
+          text: JSON.stringify(response),
+        },
+      ],
+    };
+  },
+);
+
+server.registerPrompt(
+  'poem-writer',
+  {
+    title: 'Poem Writer',
+    description: 'Write a nice haiku',
+    argsSchema: { title: z.string(), mood: z.string().optional() },
+  },
+  ({ title, mood }) => ({
+    messages: [
+      {
+        role: 'user',
+        content: {
+          type: 'text',
+          text: `Write a haiku${mood ? ` with the mood ${mood}` : ''} called ${title}. Note that a haiku is 5 syllables followed by 7 syllables followed by 5 syllables `,
+        },
+      },
+    ],
+  }),
+);
+
+const transport = new StdioServerTransport();
+await server.connect(transport);

packages/cli/src/commands/extensions/examples/mcp-server/gemini-extension.json

@@ -0,0 +1,10 @@
+{
+  "name": "mcp-server",
+  "version": "1.0.0",
+  "mcpServers": {
+    "nodeServer": {
+      "command": "node",
+      "args": ["${extensionPath}${/}example.ts"]
+    }
+  }
+}

packages/cli/src/commands/extensions/install.test.ts

@@ -8,18 +8,22 @@ import { describe, it, expect } from 'vitest';
 import { installCommand } from './install.js';
 import yargs from 'yargs';
 
+vi.mock('../../config/extension.js', () => ({
+  installExtension: vi.fn(),
+}));
+
 describe('extensions install command', () => {
   it('should fail if no source is provided', () => {
     const validationParser = yargs([]).command(installCommand).fail(false);
     expect(() => validationParser.parse('install')).toThrow(
-      'Either a git URL --source or a --path must be provided.',
+      'Either source or --path must be provided.',
     );
   });
 
   it('should fail if both git source and local path are provided', () => {
     const validationParser = yargs([]).command(installCommand).fail(false);
     expect(() =>
-      validationParser.parse('install --source some-url --path /some/path'),
+      validationParser.parse('install some-url --path /some/path'),
     ).toThrow('Arguments source and path are mutually exclusive');
   });
 });

packages/cli/src/commands/extensions/install.ts

@@ -19,14 +19,34 @@ interface InstallArgs {
 
 export async function handleInstall(args: InstallArgs) {
   try {
-    const installMetadata: ExtensionInstallMetadata = {
-      source: (args.source || args.path) as string,
-      type: args.source ? 'git' : 'local',
-    };
-    const extensionName = await installExtension(installMetadata);
-    console.log(
-      `Extension "${extensionName}" installed successfully and enabled.`,
-    );
+    let installMetadata: ExtensionInstallMetadata;
+
+    if (args.source) {
+      const { source } = args;
+      if (
+        source.startsWith('http://') ||
+        source.startsWith('https://') ||
+        source.startsWith('git@')
+      ) {
+        installMetadata = {
+          source,
+          type: 'git',
+        };
+      } else {
+        throw new Error(`The source "${source}" is not a valid URL format.`);
+      }
+    } else if (args.path) {
+      installMetadata = {
+        source: args.path,
+        type: 'local',
+      };
+    } else {
+      // This should not be reached due to the yargs check.
+      throw new Error('Either --source or --path must be provided.');
+    }
+
+    const name = await installExtension(installMetadata);
+    console.log(`Extension "${name}" installed successfully and enabled.`);
   } catch (error) {
     console.error(getErrorMessage(error));
     process.exit(1);
@@ -34,12 +54,12 @@ export async function handleInstall(args: InstallArgs) {
 }
 
 export const installCommand: CommandModule = {
-  command: 'install [--source | --path ]',
-  describe: 'Installs an extension from a git repository or a local path.',
+  command: 'install [source]',
+  describe: 'Installs an extension from a git repository URL or a local path.',
   builder: (yargs) =>
     yargs
-      .option('source', {
-        describe: 'The git URL of the extension to install.',
+      .positional('source', {
+        describe: 'The github URL of the extension to install.',
         type: 'string',
       })
       .option('path', {
@@ -49,9 +69,7 @@ export const installCommand: CommandModule = {
       .conflicts('source', 'path')
       .check((argv) => {
         if (!argv.source && !argv.path) {
-          throw new Error(
-            'Either a git URL --source or a --path must be provided.',
-          );
+          throw new Error('Either source or --path must be provided.');
         }
         return true;
       }),

packages/cli/src/commands/extensions/link.ts

@@ -0,0 +1,51 @@
+/**
+ * @license
+ * Copyright 2025 Google LLC
+ * SPDX-License-Identifier: Apache-2.0
+ */
+
+import type { CommandModule } from 'yargs';
+import {
+  installExtension,
+  type ExtensionInstallMetadata,
+} from '../../config/extension.js';
+
+import { getErrorMessage } from '../../utils/errors.js';
+
+interface InstallArgs {
+  path: string;
+}
+
+export async function handleLink(args: InstallArgs) {
+  try {
+    const installMetadata: ExtensionInstallMetadata = {
+      source: args.path,
+      type: 'link',
+    };
+    const extensionName = await installExtension(installMetadata);
+    console.log(
+      `Extension "${extensionName}" linked successfully and enabled.`,
+    );
+  } catch (error) {
+    console.error(getErrorMessage(error));
+    process.exit(1);
+  }
+}
+
+export const linkCommand: CommandModule = {
+  command: 'link <path>',
+  describe:
+    'Links an extension from a local path. Updates made to the local path will always be reflected.',
+  builder: (yargs) =>
+    yargs
+      .positional('path', {
+        describe: 'The name of the extension to link.',
+        type: 'string',
+      })
+      .check((_) => true),
+  handler: async (argv) => {
+    await handleLink({
+      path: argv['path'] as string,
+    });
+  },
+};

packages/cli/src/commands/extensions/new.test.ts

@@ -0,0 +1,73 @@
+/**
+ * @license
+ * Copyright 2025 Google LLC
+ * SPDX-License-Identifier: Apache-2.0
+ */
+
+import { describe, it, expect, vi, beforeEach } from 'vitest';
+import { newCommand } from './new.js';
+import yargs from 'yargs';
+import * as fsPromises from 'node:fs/promises';
+
+vi.mock('node:fs/promises');
+
+const mockedFs = vi.mocked(fsPromises);
+
+describe('extensions new command', () => {
+  beforeEach(() => {
+    vi.resetAllMocks();
+
+    const fakeFiles = [
+      { name: 'context', isDirectory: () => true },
+      { name: 'custom-commands', isDirectory: () => true },
+      { name: 'mcp-server', isDirectory: () => true },
+    ];
+    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+    mockedFs.readdir.mockResolvedValue(fakeFiles as any);
+  });
+
+  it('should fail if no path is provided', async () => {
+    const parser = yargs([]).command(newCommand).fail(false);
+    await expect(parser.parseAsync('new')).rejects.toThrow(
+      'Not enough non-option arguments: got 0, need at least 2',
+    );
+  });
+
+  it('should fail if no template is provided', async () => {
+    const parser = yargs([]).command(newCommand).fail(false);
+    await expect(parser.parseAsync('new /some/path')).rejects.toThrow(
+      'Not enough non-option arguments: got 1, need at least 2',
+    );
+  });
+
+  it('should create directory and copy files when path does not exist', async () => {
+    mockedFs.access.mockRejectedValue(new Error('ENOENT'));
+    mockedFs.mkdir.mockResolvedValue(undefined);
+    mockedFs.cp.mockResolvedValue(undefined);
+
+    const parser = yargs([]).command(newCommand).fail(false);
+
+    await parser.parseAsync('new /some/path context');
+
+    expect(mockedFs.mkdir).toHaveBeenCalledWith('/some/path', {
+      recursive: true,
+    });
+    expect(mockedFs.cp).toHaveBeenCalledWith(
+      expect.stringContaining('context'),
+      '/some/path',
+      { recursive: true },
+    );
+  });
+
+  it('should throw an error if the path already exists', async () => {
+    mockedFs.access.mockResolvedValue(undefined);
+    const parser = yargs([]).command(newCommand).fail(false);
+
+    await expect(parser.parseAsync('new /some/path context')).rejects.toThrow(
+      'Path already exists: /some/path',
+    );
+
+    expect(mockedFs.mkdir).not.toHaveBeenCalled();
+    expect(mockedFs.cp).not.toHaveBeenCalled();
+  });
+});

packages/cli/src/commands/extensions/new.ts

@@ -0,0 +1,86 @@
+/**
+ * @license
+ * Copyright 2025 Google LLC
+ * SPDX-License-Identifier: Apache-2.0
+ */
+
+import { access, cp, mkdir, readdir } from 'node:fs/promises';
+import { join, dirname } from 'node:path';
+import type { CommandModule } from 'yargs';
+import { fileURLToPath } from 'node:url';
+import { getErrorMessage } from '../../utils/errors.js';
+
+interface NewArgs {
+  path: string;
+  template: string;
+}
+
+const __filename = fileURLToPath(import.meta.url);
+const __dirname = dirname(__filename);
+
+const EXAMPLES_PATH = join(__dirname, 'examples');
+
+async function pathExists(path: string) {
+  try {
+    await access(path);
+    return true;
+  } catch (_e) {
+    return false;
+  }
+}
+
+async function copyDirectory(template: string, path: string) {
+  if (await pathExists(path)) {
+    throw new Error(`Path already exists: ${path}`);
+  }
+
+  const examplePath = join(EXAMPLES_PATH, template);
+  await mkdir(path, { recursive: true });
+  await cp(examplePath, path, { recursive: true });
+}
+
+async function handleNew(args: NewArgs) {
+  try {
+    await copyDirectory(args.template, args.path);
+    console.log(
+      `Successfully created new extension from template "${args.template}" at ${args.path}.`,
+    );
+    console.log(
+      `You can install this using "gemini extensions link ${args.path}" to test it out.`,
+    );
+  } catch (error) {
+    console.error(getErrorMessage(error));
+    throw error;
+  }
+}
+
+async function getBoilerplateChoices() {
+  const entries = await readdir(EXAMPLES_PATH, { withFileTypes: true });
+  return entries
+    .filter((entry) => entry.isDirectory())
+    .map((entry) => entry.name);
+}
+
+export const newCommand: CommandModule = {
+  command: 'new <path> <template>',
+  describe: 'Create a new extension from a boilerplate example.',
+  builder: async (yargs) => {
+    const choices = await getBoilerplateChoices();
+    return yargs
+      .positional('path', {
+        describe: 'The path to create the extension in.',
+        type: 'string',
+      })
+      .positional('template', {
+        describe: 'The boilerplate template to use.',
+        type: 'string',
+        choices,
+      });
+  },
+  handler: async (args) => {
+    await handleNew({
+      path: args['path'] as string,
+      template: args['template'] as string,
+    });
+  },
+};

packages/cli/src/commands/extensions/update.ts

@@ -5,43 +5,71 @@
  */
 
 import type { CommandModule } from 'yargs';
-import { updateExtension } from '../../config/extension.js';
+import {
+  updateExtensionByName,
+  updateAllUpdatableExtensions,
+  type ExtensionUpdateInfo,
+} from '../../config/extension.js';
 import { getErrorMessage } from '../../utils/errors.js';
 
 interface UpdateArgs {
-  name: string;
+  name?: string;
+  all?: boolean;
 }
 
+const updateOutput = (info: ExtensionUpdateInfo) =>
+  `Extension "${info.name}" successfully updated: ${info.originalVersion} → ${info.updatedVersion}.`;
+
 export async function handleUpdate(args: UpdateArgs) {
-  try {
-    // TODO(chrstnb): we should list extensions if the requested extension is not installed.
-    const updatedExtensionInfo = await updateExtension(args.name);
-    if (!updatedExtensionInfo) {
-      console.log(`Extension "${args.name}" failed to update.`);
-      return;
+  if (args.all) {
+    try {
+      const updateInfos = await updateAllUpdatableExtensions();
+      if (updateInfos.length === 0) {
+        console.log('No extensions to update.');
+        return;
+      }
+      console.log(updateInfos.map((info) => updateOutput(info)).join('\n'));
+    } catch (error) {
+      console.error(getErrorMessage(error));
     }
-    console.log(
-      `Extension "${args.name}" successfully updated: ${updatedExtensionInfo.originalVersion} → ${updatedExtensionInfo.updatedVersion}.`,
-    );
-  } catch (error) {
-    console.error(getErrorMessage(error));
-    process.exit(1);
   }
+  if (args.name)
+    try {
+      // TODO(chrstnb): we should list extensions if the requested extension is not installed.
+      const updatedExtensionInfo = await updateExtensionByName(args.name);
+      console.log(
+        `Extension "${args.name}" successfully updated: ${updatedExtensionInfo.originalVersion} → ${updatedExtensionInfo.updatedVersion}.`,
+      );
+    } catch (error) {
+      console.error(getErrorMessage(error));
+    }
 }
 
 export const updateCommand: CommandModule = {
-  command: 'update <name>',
-  describe: 'Updates an extension.',
+  command: 'update [--all] [name]',
+  describe:
+    'Updates all extensions or a named extension to the latest version.',
   builder: (yargs) =>
     yargs
       .positional('name', {
         describe: 'The name of the extension to update.',
         type: 'string',
       })
-      .check((_argv) => true),
+      .option('all', {
+        describe: 'Update all extensions.',
+        type: 'boolean',
+      })
+      .conflicts('name', 'all')
+      .check((argv) => {
+        if (!argv.all && !argv.name) {
+          throw new Error('Either an extension name or --all must be provided');
+        }
+        return true;
+      }),
   handler: async (argv) => {
     await handleUpdate({
-      name: argv['name'] as string,
+      name: argv['name'] as string | undefined,
+      all: argv['all'] as boolean | undefined,
     });
   },
 };

packages/cli/src/commands/mcp/add.ts

@@ -38,7 +38,7 @@ async function addMcpServer(
   } = options;
   const settingsScope =
     scope === 'user' ? SettingScope.User : SettingScope.Workspace;
-  const settings = loadSettings(process.cwd());
+  const settings = loadSettings();
 
   let newServer: Partial<MCPServerConfig> = {};
 

packages/cli/src/commands/mcp/list.ts

@@ -20,8 +20,8 @@ const RESET_COLOR = '\u001b[0m';
 async function getMcpServersFromConfig(): Promise<
   Record<string, MCPServerConfig>
 > {
-  const settings = loadSettings(process.cwd());
-  const extensions = loadExtensions(process.cwd());
+  const settings = loadSettings();
+  const extensions = loadExtensions();
   const mcpServers = { ...(settings.merged.mcpServers || {}) };
   for (const extension of extensions) {
     Object.entries(extension.config.mcpServers || {}).forEach(

packages/cli/src/commands/mcp/remove.ts

@@ -17,7 +17,7 @@ async function removeMcpServer(
   const { scope } = options;
   const settingsScope =
     scope === 'user' ? SettingScope.User : SettingScope.Workspace;
-  const settings = loadSettings(process.cwd());
+  const settings = loadSettings();
 
   const existingSettings = settings.forScope(settingsScope).settings;
   const mcpServers = existingSettings.mcpServers || {};

packages/cli/src/config/auth.test.ts

@@ -10,18 +10,22 @@ import { validateAuthMethod } from './auth.js';
 
 vi.mock('./settings.js', () => ({
   loadEnvironment: vi.fn(),
+  loadSettings: vi.fn().mockReturnValue({
+    merged: vi.fn().mockReturnValue({}),
+  }),
 }));
 
 describe('validateAuthMethod', () => {
-  const originalEnv = process.env;
-
   beforeEach(() => {
     vi.resetModules();
-    process.env = {};
+    vi.stubEnv('GEMINI_API_KEY', undefined);
+    vi.stubEnv('GOOGLE_CLOUD_PROJECT', undefined);
+    vi.stubEnv('GOOGLE_CLOUD_LOCATION', undefined);
+    vi.stubEnv('GOOGLE_API_KEY', undefined);
   });
 
   afterEach(() => {
-    process.env = originalEnv;
+    vi.unstubAllEnvs();
   });
 
   it('should return null for LOGIN_WITH_GOOGLE', () => {
@@ -34,11 +38,12 @@ describe('validateAuthMethod', () => {
 
   describe('USE_GEMINI', () => {
     it('should return null if GEMINI_API_KEY is set', () => {
-      process.env['GEMINI_API_KEY'] = 'test-key';
+      vi.stubEnv('GEMINI_API_KEY', 'test-key');
       expect(validateAuthMethod(AuthType.USE_GEMINI)).toBeNull();
     });
 
     it('should return an error message if GEMINI_API_KEY is not set', () => {
+      vi.stubEnv('GEMINI_API_KEY', undefined);
       expect(validateAuthMethod(AuthType.USE_GEMINI)).toBe(
         'GEMINI_API_KEY environment variable not found. Add that to your environment and try again (no reload needed if using .env)!',
       );
@@ -47,17 +52,19 @@ describe('validateAuthMethod', () => {
 
   describe('USE_VERTEX_AI', () => {
     it('should return null if GOOGLE_CLOUD_PROJECT and GOOGLE_CLOUD_LOCATION are set', () => {
-      process.env['GOOGLE_CLOUD_PROJECT'] = 'test-project';
-      process.env['GOOGLE_CLOUD_LOCATION'] = 'test-location';
+      vi.stubEnv('GOOGLE_CLOUD_PROJECT', 'test-project');
+      vi.stubEnv('GOOGLE_CLOUD_LOCATION', 'test-location');
       expect(validateAuthMethod(AuthType.USE_VERTEX_AI)).toBeNull();
     });
 
     it('should return null if GOOGLE_API_KEY is set', () => {
-      process.env['GOOGLE_API_KEY'] = 'test-api-key';
+      vi.stubEnv('GOOGLE_API_KEY', 'test-api-key');
       expect(validateAuthMethod(AuthType.USE_VERTEX_AI)).toBeNull();
     });
 
     it('should return an error message if no required environment variables are set', () => {
+      vi.stubEnv('GOOGLE_CLOUD_PROJECT', undefined);
+      vi.stubEnv('GOOGLE_CLOUD_LOCATION', undefined);
       expect(validateAuthMethod(AuthType.USE_VERTEX_AI)).toBe(
         'When using Vertex AI, you must specify either:\n' +
           '• GOOGLE_CLOUD_PROJECT and GOOGLE_CLOUD_LOCATION environment variables.\n' +

packages/cli/src/config/auth.ts

@@ -5,10 +5,10 @@
  */
 
 import { AuthType } from '@google/gemini-cli-core';
-import { loadEnvironment } from './settings.js';
+import { loadEnvironment, loadSettings } from './settings.js';
 
-export const validateAuthMethod = (authMethod: string): string | null => {
-  loadEnvironment();
+export function validateAuthMethod(authMethod: string): string | null {
+  loadEnvironment(loadSettings().merged);
   if (
     authMethod === AuthType.LOGIN_WITH_GOOGLE ||
     authMethod === AuthType.CLOUD_SHELL
@@ -40,4 +40,4 @@ export const validateAuthMethod = (authMethod: string): string | null => {
   }
 
   return 'Invalid auth method selected.';
-};
+}

packages/cli/src/config/config.test.ts

@@ -4,15 +4,7 @@
  * SPDX-License-Identifier: Apache-2.0
  */
 
-import {
-  describe,
-  it,
-  expect,
-  vi,
-  beforeEach,
-  afterEach,
-  type Mock,
-} from 'vitest';
+import { describe, it, expect, vi, beforeEach, afterEach } from 'vitest';
 import * as os from 'node:os';
 import * as path from 'node:path';
 import { ShellTool, EditTool, WriteFileTool } from '@google/gemini-cli-core';
@@ -723,6 +715,7 @@ describe('Hierarchical Memory Loading (config.ts) - Placeholder Suite', () => {
         '/path/to/ext3/context1.md',
         '/path/to/ext3/context2.md',
       ],
+      true,
       'tree',
       {
         respectGitIgnore: false,
@@ -1491,40 +1484,6 @@ describe('loadCliConfig model selection', () => {
   });
 });
 
-describe('loadCliConfig folderTrustFeature', () => {
-  const originalArgv = process.argv;
-
-  beforeEach(() => {
-    vi.resetAllMocks();
-    vi.mocked(os.homedir).mockReturnValue('/mock/home/user');
-    vi.stubEnv('GEMINI_API_KEY', 'test-api-key');
-  });
-
-  afterEach(() => {
-    process.argv = originalArgv;
-    vi.unstubAllEnvs();
-    vi.restoreAllMocks();
-  });
-
-  it('should be false by default', async () => {
-    process.argv = ['node', 'script.js'];
-    const settings: Settings = {};
-    const argv = await parseArguments({} as Settings);
-    const config = await loadCliConfig(settings, [], 'test-session', argv);
-    expect(config.getFolderTrustFeature()).toBe(false);
-  });
-
-  it('should be true when settings.folderTrustFeature is true', async () => {
-    process.argv = ['node', 'script.js'];
-    const argv = await parseArguments({} as Settings);
-    const settings: Settings = {
-      security: { folderTrust: { featureEnabled: true } },
-    };
-    const config = await loadCliConfig(settings, [], 'test-session', argv);
-    expect(config.getFolderTrustFeature()).toBe(true);
-  });
-});
-
 describe('loadCliConfig folderTrust', () => {
   const originalArgv = process.argv;
 
@@ -1540,12 +1499,11 @@ describe('loadCliConfig folderTrust', () => {
     vi.restoreAllMocks();
   });
 
-  it('should be false if folderTrustFeature is false and folderTrust is false', async () => {
+  it('should be false when folderTrust is false', async () => {
     process.argv = ['node', 'script.js'];
     const settings: Settings = {
       security: {
         folderTrust: {
-          featureEnabled: false,
           enabled: false,
         },
       },
@@ -1555,43 +1513,12 @@ describe('loadCliConfig folderTrust', () => {
     expect(config.getFolderTrust()).toBe(false);
   });
 
-  it('should be false if folderTrustFeature is true and folderTrust is false', async () => {
+  it('should be true when folderTrust is true', async () => {
     process.argv = ['node', 'script.js'];
     const argv = await parseArguments({} as Settings);
     const settings: Settings = {
       security: {
         folderTrust: {
-          featureEnabled: true,
-          enabled: false,
-        },
-      },
-    };
-    const config = await loadCliConfig(settings, [], 'test-session', argv);
-    expect(config.getFolderTrust()).toBe(false);
-  });
-
-  it('should be false if folderTrustFeature is false and folderTrust is true', async () => {
-    process.argv = ['node', 'script.js'];
-    const argv = await parseArguments({} as Settings);
-    const settings: Settings = {
-      security: {
-        folderTrust: {
-          featureEnabled: false,
-          enabled: true,
-        },
-      },
-    };
-    const config = await loadCliConfig(settings, [], 'test-session', argv);
-    expect(config.getFolderTrust()).toBe(false);
-  });
-
-  it('should be true when folderTrustFeature is true and folderTrust is true', async () => {
-    process.argv = ['node', 'script.js'];
-    const argv = await parseArguments({} as Settings);
-    const settings: Settings = {
-      security: {
-        folderTrust: {
-          featureEnabled: true,
           enabled: true,
         },
       },
@@ -1599,6 +1526,14 @@ describe('loadCliConfig folderTrust', () => {
     const config = await loadCliConfig(settings, [], 'test-session', argv);
     expect(config.getFolderTrust()).toBe(true);
   });
+
+  it('should be false by default', async () => {
+    process.argv = ['node', 'script.js'];
+    const argv = await parseArguments({} as Settings);
+    const settings: Settings = {};
+    const config = await loadCliConfig(settings, [], 'test-session', argv);
+    expect(config.getFolderTrust()).toBe(false);
+  });
 });
 
 describe('loadCliConfig with includeDirectories', () => {
@@ -1959,7 +1894,7 @@ describe('loadCliConfig approval mode', () => {
   });
 });
 
-describe('loadCliConfig trustedFolder', () => {
+describe('loadCliConfig fileFiltering', () => {
   const originalArgv = process.argv;
 
   beforeEach(() => {
@@ -1975,120 +1910,116 @@ describe('loadCliConfig trustedFolder', () => {
     vi.restoreAllMocks();
   });
 
-  const testCases = [
-    // Cases where folderTrustFeature is false (feature disabled)
+  const testCases: Array<{
+    property: keyof NonNullable<Settings['fileFiltering']>;
+    getter: (config: ServerConfig.Config) => boolean;
+    value: boolean;
+  }> = [
     {
-      folderTrustFeature: false,
-      folderTrust: true,
-      isWorkspaceTrusted: true,
-      expectedFolderTrust: false,
-      expectedIsTrustedFolder: true,
-      description:
-        'feature disabled, folderTrust true, workspace trusted -> behave as trusted',
+      property: 'disableFuzzySearch',
+      getter: (c) => c.getFileFilteringDisableFuzzySearch(),
+      value: true,
     },
     {
-      folderTrustFeature: false,
-      folderTrust: true,
-      isWorkspaceTrusted: false,
-      expectedFolderTrust: false,
-      expectedIsTrustedFolder: true,
-      description:
-        'feature disabled, folderTrust true, workspace not trusted -> behave as trusted',
+      property: 'disableFuzzySearch',
+      getter: (c) => c.getFileFilteringDisableFuzzySearch(),
+      value: false,
     },
     {
-      folderTrustFeature: false,
-      folderTrust: false,
-      isWorkspaceTrusted: true,
-      expectedFolderTrust: false,
-      expectedIsTrustedFolder: true,
-      description:
-        'feature disabled, folderTrust false, workspace trusted -> behave as trusted',
-    },
-
-    // Cases where folderTrustFeature is true but folderTrust setting is false
-    {
-      folderTrustFeature: true,
-      folderTrust: false,
-      isWorkspaceTrusted: true,
-      expectedFolderTrust: false,
-      expectedIsTrustedFolder: true,
-      description:
-        'feature on, folderTrust false, workspace trusted -> behave as trusted',
+      property: 'respectGitIgnore',
+      getter: (c) => c.getFileFilteringRespectGitIgnore(),
+      value: true,
     },
     {
-      folderTrustFeature: true,
-      folderTrust: false,
-      isWorkspaceTrusted: false,
-      expectedFolderTrust: false,
-      expectedIsTrustedFolder: true,
-      description:
-        'feature on, folderTrust false, workspace not trusted -> behave as trusted',
-    },
-
-    // Cases where feature is fully enabled (folderTrustFeature and folderTrust are true)
-    {
-      folderTrustFeature: true,
-      folderTrust: true,
-      isWorkspaceTrusted: true,
-      expectedFolderTrust: true,
-      expectedIsTrustedFolder: true,
-      description:
-        'feature on, folderTrust on, workspace trusted -> is trusted',
+      property: 'respectGitIgnore',
+      getter: (c) => c.getFileFilteringRespectGitIgnore(),
+      value: false,
     },
     {
-      folderTrustFeature: true,
-      folderTrust: true,
-      isWorkspaceTrusted: false,
-      expectedFolderTrust: true,
-      expectedIsTrustedFolder: false,
-      description:
-        'feature on, folderTrust on, workspace NOT trusted -> is NOT trusted',
+      property: 'respectGeminiIgnore',
+      getter: (c) => c.getFileFilteringRespectGeminiIgnore(),
+      value: true,
     },
     {
-      folderTrustFeature: true,
-      folderTrust: true,
-      isWorkspaceTrusted: undefined,
-      expectedFolderTrust: true,
-      expectedIsTrustedFolder: undefined,
-      description:
-        'feature on, folderTrust on, workspace trust unknown -> is unknown',
+      property: 'respectGeminiIgnore',
+      getter: (c) => c.getFileFilteringRespectGeminiIgnore(),
+      value: false,
+    },
+    {
+      property: 'enableRecursiveFileSearch',
+      getter: (c) => c.getEnableRecursiveFileSearch(),
+      value: true,
+    },
+    {
+      property: 'enableRecursiveFileSearch',
+      getter: (c) => c.getEnableRecursiveFileSearch(),
+      value: false,
     },
   ];
 
-  for (const {
-    folderTrustFeature,
-    folderTrust,
-    isWorkspaceTrusted: mockTrustValue,
-    expectedFolderTrust,
-    expectedIsTrustedFolder,
-    description,
-  } of testCases) {
-    it(`should be correct for: ${description}`, async () => {
-      (isWorkspaceTrusted as Mock).mockImplementation((settings: Settings) => {
-        const folderTrustFeature =
-          settings.security?.folderTrust?.featureEnabled ?? false;
-        const folderTrustSetting =
-          settings.security?.folderTrust?.enabled ?? true;
-        const folderTrustEnabled = folderTrustFeature && folderTrustSetting;
-
-        if (!folderTrustEnabled) {
-          return true;
-        }
-        return mockTrustValue; // This is the part that comes from the test case
-      });
-      const argv = await parseArguments({} as Settings);
+  it.each(testCases)(
+    'should pass $property from settings to config when $value',
+    async ({ property, getter, value }) => {
       const settings: Settings = {
-        security: {
-          folderTrust: {
-            featureEnabled: folderTrustFeature,
-            enabled: folderTrust,
-          },
+        context: {
+          fileFiltering: { [property]: value },
         },
       };
+      const argv = await parseArguments(settings);
       const config = await loadCliConfig(settings, [], 'test-session', argv);
-
-      expect(config.getFolderTrust()).toBe(expectedFolderTrust);
-      expect(config.isTrustedFolder()).toBe(expectedIsTrustedFolder);
-    });
-  }
+      expect(getter(config)).toBe(value);
+    },
+  );
+});
+
+describe('parseArguments with positional prompt', () => {
+  const originalArgv = process.argv;
+
+  afterEach(() => {
+    process.argv = originalArgv;
+  });
+
+  it('should throw an error when both a positional prompt and the --prompt flag are used', async () => {
+    process.argv = [
+      'node',
+      'script.js',
+      'positional',
+      'prompt',
+      '--prompt',
+      'test prompt',
+    ];
+
+    const mockExit = vi.spyOn(process, 'exit').mockImplementation(() => {
+      throw new Error('process.exit called');
+    });
+
+    const mockConsoleError = vi
+      .spyOn(console, 'error')
+      .mockImplementation(() => {});
+
+    await expect(parseArguments({} as Settings)).rejects.toThrow(
+      'process.exit called',
+    );
+
+    expect(mockConsoleError).toHaveBeenCalledWith(
+      expect.stringContaining(
+        'Cannot use both a positional prompt and the --prompt (-p) flag together',
+      ),
+    );
+
+    mockExit.mockRestore();
+    mockConsoleError.mockRestore();
+  });
+
+  it('should correctly parse a positional prompt', async () => {
+    process.argv = ['node', 'script.js', 'positional', 'prompt'];
+    const argv = await parseArguments({} as Settings);
+    expect(argv.promptWords).toEqual(['positional', 'prompt']);
+  });
+
+  it('should correctly parse a prompt from the --prompt flag', async () => {
+    process.argv = ['node', 'script.js', '--prompt', 'test prompt'];
+    const argv = await parseArguments({} as Settings);
+    expect(argv.prompt).toBe('test prompt');
+  });
 });

packages/cli/src/config/config.ts

@@ -38,6 +38,7 @@ import { annotateActiveExtensions } from './extension.js';
 import { getCliVersion } from '../utils/version.js';
 import { loadSandboxConfig } from './sandboxConfig.js';
 import { resolvePath } from '../utils/resolvePath.js';
+import { appEvents } from '../utils/events.js';
 
 import { isWorkspaceTrusted } from './trustedFolders.js';
 
@@ -77,6 +78,9 @@ export interface CliArgs {
   proxy: string | undefined;
   includeDirectories: string[] | undefined;
   screenReader: boolean | undefined;
+  useSmartEdit: boolean | undefined;
+  sessionSummary: string | undefined;
+  promptWords: string[] | undefined;
 }
 
 export async function parseArguments(settings: Settings): Promise<CliArgs> {
@@ -86,7 +90,7 @@ export async function parseArguments(settings: Settings): Promise<CliArgs> {
     .usage(
       'Usage: gemini [options] [command]\n\nGemini CLI - Launch an interactive CLI, use -p/--prompt for non-interactive mode',
     )
-    .command('$0', 'Launch Gemini CLI', (yargsInstance) =>
+    .command('$0 [promptWords...]', 'Launch Gemini CLI', (yargsInstance) =>
       yargsInstance
         .option('model', {
           alias: 'm',
@@ -226,9 +230,66 @@ export async function parseArguments(settings: Settings): Promise<CliArgs> {
           description: 'Enable screen reader mode for accessibility.',
           default: false,
         })
-
+        .option('session-summary', {
+          type: 'string',
+          description: 'File to write session summary to.',
+        })
+        .deprecateOption(
+          'telemetry',
+          'Use the "telemetry.enabled" setting in settings.json instead. This flag will be removed in a future version.',
+        )
+        .deprecateOption(
+          'telemetry-target',
+          'Use the "telemetry.target" setting in settings.json instead. This flag will be removed in a future version.',
+        )
+        .deprecateOption(
+          'telemetry-otlp-endpoint',
+          'Use the "telemetry.otlpEndpoint" setting in settings.json instead. This flag will be removed in a future version.',
+        )
+        .deprecateOption(
+          'telemetry-otlp-protocol',
+          'Use the "telemetry.otlpProtocol" setting in settings.json instead. This flag will be removed in a future version.',
+        )
+        .deprecateOption(
+          'telemetry-log-prompts',
+          'Use the "telemetry.logPrompts" setting in settings.json instead. This flag will be removed in a future version.',
+        )
+        .deprecateOption(
+          'telemetry-outfile',
+          'Use the "telemetry.outfile" setting in settings.json instead. This flag will be removed in a future version.',
+        )
+        .deprecateOption(
+          'show-memory-usage',
+          'Use the "ui.showMemoryUsage" setting in settings.json instead. This flag will be removed in a future version.',
+        )
+        .deprecateOption(
+          'sandbox-image',
+          'Use the "tools.sandbox" setting in settings.json instead. This flag will be removed in a future version.',
+        )
+        .deprecateOption(
+          'proxy',
+          'Use the "proxy" setting in settings.json instead. This flag will be removed in a future version.',
+        )
+        .deprecateOption(
+          'checkpointing',
+          'Use the "general.checkpointing.enabled" setting in settings.json instead. This flag will be removed in a future version.',
+        )
+        .deprecateOption(
+          'all-files',
+          'Use @ includes in the application instead. This flag will be removed in a future version.',
+        )
+        .deprecateOption(
+          'prompt',
+          'Use the positional prompt instead. This flag will be removed in a future version.',
+        )
         .check((argv) => {
-          if (argv.prompt && argv['promptInteractive']) {
+          const promptWords = argv['promptWords'] as string[] | undefined;
+          if (argv['prompt'] && promptWords && promptWords.length > 0) {
+            throw new Error(
+              'Cannot use both a positional prompt and the --prompt (-p) flag together',
+            );
+          }
+          if (argv['prompt'] && argv['promptInteractive']) {
             throw new Error(
               'Cannot use both --prompt (-p) and --prompt-interactive (-i) together',
             );
@@ -244,7 +305,7 @@ export async function parseArguments(settings: Settings): Promise<CliArgs> {
     // Register MCP subcommands
     .command(mcpCommand);
 
-  if (settings?.experimental?.extensionManagement ?? false) {
+  if (settings?.experimental?.extensionManagement ?? true) {
     yargsInstance.command(extensionsCommand);
   }
 
@@ -284,6 +345,7 @@ export async function loadHierarchicalGeminiMemory(
   fileService: FileDiscoveryService,
   settings: Settings,
   extensionContextFilePaths: string[] = [],
+  folderTrust: boolean,
   memoryImportFormat: 'flat' | 'tree' = 'tree',
   fileFilteringOptions?: FileFilteringOptions,
 ): Promise<{ memoryContent: string; fileCount: number }> {
@@ -309,6 +371,7 @@ export async function loadHierarchicalGeminiMemory(
     debugMode,
     fileService,
     extensionContextFilePaths,
+    folderTrust,
     memoryImportFormat,
     fileFilteringOptions,
     settings.context?.discoveryMaxDirs,
@@ -332,11 +395,8 @@ export async function loadCliConfig(
 
   const ideMode = settings.ide?.enabled ?? false;
 
-  const folderTrustFeature =
-    settings.security?.folderTrust?.featureEnabled ?? false;
-  const folderTrustSetting = settings.security?.folderTrust?.enabled ?? true;
-  const folderTrust = folderTrustFeature && folderTrustSetting;
-  const trustedFolder = isWorkspaceTrusted(settings);
+  const folderTrust = settings.security?.folderTrust?.enabled ?? false;
+  const trustedFolder = isWorkspaceTrusted(settings) ?? true;
 
   const allExtensions = annotateActiveExtensions(
     extensions,
@@ -384,12 +444,14 @@ export async function loadCliConfig(
     fileService,
     settings,
     extensionContextFilePaths,
+    trustedFolder,
     memoryImportFormat,
     fileFiltering,
   );
 
   let mcpServers = mergeMcpServers(settings, activeExtensions);
-  const question = argv.promptInteractive || argv.prompt || '';
+  const question =
+    argv.promptInteractive || argv.prompt || (argv.promptWords || []).join(' ');
 
   // Determine approval mode with backward compatibility
   let approvalMode: ApprovalMode;
@@ -530,14 +592,7 @@ export async function loadCliConfig(
       outfile: argv.telemetryOutfile ?? settings.telemetry?.outfile,
     },
     usageStatisticsEnabled: settings.privacy?.usageStatisticsEnabled ?? true,
-    // Git-aware file filtering settings
-    fileFiltering: {
-      respectGitIgnore: settings.context?.fileFiltering?.respectGitIgnore,
-      respectGeminiIgnore: settings.context?.fileFiltering?.respectGeminiIgnore,
-      enableRecursiveFileSearch:
-        settings.context?.fileFiltering?.enableRecursiveFileSearch,
-      disableFuzzySearch: settings.context?.fileFiltering?.disableFuzzySearch,
-    },
+    fileFiltering: settings.context?.fileFiltering,
     checkpointing:
       argv.checkpointing || settings.general?.checkpointing?.enabled,
     proxy:
@@ -560,7 +615,6 @@ export async function loadCliConfig(
     summarizeToolOutput: settings.model?.summarizeToolOutput,
     ideMode,
     chatCompression: settings.model?.chatCompression,
-    folderTrustFeature,
     folderTrust,
     interactive,
     trustedFolder,
@@ -568,6 +622,11 @@ export async function loadCliConfig(
     shouldUseNodePtyShell: settings.tools?.usePty,
     skipNextSpeakerCheck: settings.model?.skipNextSpeakerCheck,
     enablePromptCompletion: settings.general?.enablePromptCompletion ?? false,
+    truncateToolOutputThreshold: settings.tools?.truncateToolOutputThreshold,
+    truncateToolOutputLines: settings.tools?.truncateToolOutputLines,
+    enableToolOutputTruncation: settings.tools?.enableToolOutputTruncation,
+    eventEmitter: appEvents,
+    useSmartEdit: argv.useSmartEdit ?? settings.useSmartEdit,
   });
 }
 

packages/cli/src/config/extension.test.ts

@@ -20,14 +20,19 @@ import {
   performWorkspaceExtensionMigration,
   uninstallExtension,
   updateExtension,
+  type Extension,
 } from './extension.js';
 import {
+  GEMINI_DIR,
   type GeminiCLIExtension,
   type MCPServerConfig,
+  ClearcutLogger,
+  type Config,
 } from '@google/gemini-cli-core';
 import { execSync } from 'node:child_process';
 import { SettingScope, loadSettings } from './settings.js';
 import { type SimpleGit, simpleGit } from 'simple-git';
+import { isWorkspaceTrusted } from './trustedFolders.js';
 
 vi.mock('simple-git', () => ({
   simpleGit: vi.fn(),
@@ -41,6 +46,30 @@ vi.mock('os', async (importOriginal) => {
   };
 });
 
+vi.mock('./trustedFolders.js', async (importOriginal) => {
+  const actual = await importOriginal<typeof import('./trustedFolders.js')>();
+  return {
+    ...actual,
+    isWorkspaceTrusted: vi.fn(),
+  };
+});
+
+vi.mock('@google/gemini-cli-core', async (importOriginal) => {
+  const actual =
+    await importOriginal<typeof import('@google/gemini-cli-core')>();
+  const mockLogExtensionInstallEvent = vi.fn();
+  return {
+    ...actual,
+    ClearcutLogger: {
+      getInstance: vi.fn(() => ({
+        logExtensionInstallEvent: mockLogExtensionInstallEvent,
+      })),
+    },
+    Config: vi.fn(),
+    ExtensionInstallEvent: vi.fn(),
+  };
+});
+
 vi.mock('child_process', async (importOriginal) => {
   const actual = await importOriginal<typeof import('child_process')>();
   return {
@@ -49,157 +78,267 @@ vi.mock('child_process', async (importOriginal) => {
   };
 });
 
-const EXTENSIONS_DIRECTORY_NAME = path.join('.gemini', 'extensions');
+const EXTENSIONS_DIRECTORY_NAME = path.join(GEMINI_DIR, 'extensions');
 
 describe('loadExtensions', () => {
-  let tempWorkspaceDir: string;
   let tempHomeDir: string;
+  let userExtensionsDir: string;
 
   beforeEach(() => {
-    tempWorkspaceDir = fs.mkdtempSync(
-      path.join(os.tmpdir(), 'gemini-cli-test-workspace-'),
-    );
     tempHomeDir = fs.mkdtempSync(
       path.join(os.tmpdir(), 'gemini-cli-test-home-'),
     );
     vi.mocked(os.homedir).mockReturnValue(tempHomeDir);
+    vi.mocked(isWorkspaceTrusted).mockReturnValue(true);
+
+    userExtensionsDir = path.join(tempHomeDir, EXTENSIONS_DIRECTORY_NAME);
+    fs.mkdirSync(userExtensionsDir, { recursive: true });
   });
 
   afterEach(() => {
-    fs.rmSync(tempWorkspaceDir, { recursive: true, force: true });
     fs.rmSync(tempHomeDir, { recursive: true, force: true });
     vi.restoreAllMocks();
   });
 
   it('should include extension path in loaded extension', () => {
-    const workspaceExtensionsDir = path.join(
-      tempWorkspaceDir,
-      EXTENSIONS_DIRECTORY_NAME,
-    );
-    fs.mkdirSync(workspaceExtensionsDir, { recursive: true });
-
-    const extensionDir = path.join(workspaceExtensionsDir, 'test-extension');
+    const extensionDir = path.join(userExtensionsDir, 'test-extension');
     fs.mkdirSync(extensionDir, { recursive: true });
 
-    const config = {
+    createExtension({
+      extensionsDir: userExtensionsDir,
       name: 'test-extension',
       version: '1.0.0',
-    };
-    fs.writeFileSync(
-      path.join(extensionDir, EXTENSIONS_CONFIG_FILENAME),
-      JSON.stringify(config),
-    );
+    });
 
-    const extensions = loadExtensions(tempWorkspaceDir);
+    const extensions = loadExtensions();
     expect(extensions).toHaveLength(1);
     expect(extensions[0].path).toBe(extensionDir);
     expect(extensions[0].config.name).toBe('test-extension');
   });
 
   it('should load context file path when GEMINI.md is present', () => {
-    const workspaceExtensionsDir = path.join(
-      tempWorkspaceDir,
-      EXTENSIONS_DIRECTORY_NAME,
-    );
-    fs.mkdirSync(workspaceExtensionsDir, { recursive: true });
-    createExtension(workspaceExtensionsDir, 'ext1', '1.0.0', true);
-    createExtension(workspaceExtensionsDir, 'ext2', '2.0.0');
+    createExtension({
+      extensionsDir: userExtensionsDir,
+      name: 'ext1',
+      version: '1.0.0',
+      addContextFile: true,
+    });
+    createExtension({
+      extensionsDir: userExtensionsDir,
+      name: 'ext2',
+      version: '2.0.0',
+    });
 
-    const extensions = loadExtensions(tempWorkspaceDir);
+    const extensions = loadExtensions();
 
     expect(extensions).toHaveLength(2);
     const ext1 = extensions.find((e) => e.config.name === 'ext1');
     const ext2 = extensions.find((e) => e.config.name === 'ext2');
     expect(ext1?.contextFiles).toEqual([
-      path.join(workspaceExtensionsDir, 'ext1', 'GEMINI.md'),
+      path.join(userExtensionsDir, 'ext1', 'GEMINI.md'),
     ]);
     expect(ext2?.contextFiles).toEqual([]);
   });
 
   it('should load context file path from the extension config', () => {
-    const workspaceExtensionsDir = path.join(
-      tempWorkspaceDir,
-      EXTENSIONS_DIRECTORY_NAME,
-    );
-    fs.mkdirSync(workspaceExtensionsDir, { recursive: true });
-    createExtension(
-      workspaceExtensionsDir,
-      'ext1',
-      '1.0.0',
-      false,
-      'my-context-file.md',
-    );
+    createExtension({
+      extensionsDir: userExtensionsDir,
+      name: 'ext1',
+      version: '1.0.0',
+      addContextFile: false,
+      contextFileName: 'my-context-file.md',
+    });
 
-    const extensions = loadExtensions(tempWorkspaceDir);
+    const extensions = loadExtensions();
 
     expect(extensions).toHaveLength(1);
     const ext1 = extensions.find((e) => e.config.name === 'ext1');
     expect(ext1?.contextFiles).toEqual([
-      path.join(workspaceExtensionsDir, 'ext1', 'my-context-file.md'),
+      path.join(userExtensionsDir, 'ext1', 'my-context-file.md'),
     ]);
   });
 
   it('should filter out disabled extensions', () => {
-    const workspaceExtensionsDir = path.join(
-      tempWorkspaceDir,
-      EXTENSIONS_DIRECTORY_NAME,
-    );
-    fs.mkdirSync(workspaceExtensionsDir, { recursive: true });
+    createExtension({
+      extensionsDir: userExtensionsDir,
+      name: 'ext1',
+      version: '1.0.0',
+    });
+    createExtension({
+      extensionsDir: userExtensionsDir,
+      name: 'ext2',
+      version: '2.0.0',
+    });
 
-    createExtension(workspaceExtensionsDir, 'ext1', '1.0.0');
-    createExtension(workspaceExtensionsDir, 'ext2', '2.0.0');
-
-    const settingsDir = path.join(tempWorkspaceDir, '.gemini');
+    const settingsDir = path.join(tempHomeDir, GEMINI_DIR);
     fs.mkdirSync(settingsDir, { recursive: true });
     fs.writeFileSync(
       path.join(settingsDir, 'settings.json'),
       JSON.stringify({ extensions: { disabled: ['ext1'] } }),
     );
 
-    const extensions = loadExtensions(tempWorkspaceDir);
+    const extensions = loadExtensions();
     const activeExtensions = annotateActiveExtensions(
       extensions,
       [],
-      tempWorkspaceDir,
+      tempHomeDir,
     ).filter((e) => e.isActive);
     expect(activeExtensions).toHaveLength(1);
     expect(activeExtensions[0].name).toBe('ext2');
   });
 
   it('should hydrate variables', () => {
-    const workspaceExtensionsDir = path.join(
-      tempWorkspaceDir,
-      EXTENSIONS_DIRECTORY_NAME,
-    );
-    fs.mkdirSync(workspaceExtensionsDir, { recursive: true });
-
-    createExtension(
-      workspaceExtensionsDir,
-      'test-extension',
-      '1.0.0',
-      false,
-      undefined,
-      {
+    createExtension({
+      extensionsDir: userExtensionsDir,
+      name: 'test-extension',
+      version: '1.0.0',
+      addContextFile: false,
+      contextFileName: undefined,
+      mcpServers: {
         'test-server': {
           cwd: '${extensionPath}${/}server',
         },
       },
-    );
+    });
 
-    const extensions = loadExtensions(tempWorkspaceDir);
+    const extensions = loadExtensions();
     expect(extensions).toHaveLength(1);
     const loadedConfig = extensions[0].config;
     const expectedCwd = path.join(
-      workspaceExtensionsDir,
+      userExtensionsDir,
       'test-extension',
       'server',
     );
     expect(loadedConfig.mcpServers?.['test-server'].cwd).toBe(expectedCwd);
   });
+
+  it('should load a linked extension correctly', async () => {
+    const tempWorkspaceDir = fs.mkdtempSync(
+      path.join(os.tmpdir(), 'gemini-cli-test-workspace-'),
+    );
+    const sourceExtDir = createExtension({
+      extensionsDir: tempWorkspaceDir,
+      name: 'my-linked-extension',
+      version: '1.0.0',
+      contextFileName: 'context.md',
+    });
+    fs.writeFileSync(path.join(sourceExtDir, 'context.md'), 'linked context');
+
+    const extensionName = await installExtension({
+      source: sourceExtDir,
+      type: 'link',
+    });
+    expect(extensionName).toEqual('my-linked-extension');
+    const extensions = loadExtensions();
+    expect(extensions).toHaveLength(1);
+
+    const linkedExt = extensions[0];
+    expect(linkedExt.config.name).toBe('my-linked-extension');
+
+    expect(linkedExt.path).toBe(sourceExtDir);
+    expect(linkedExt.installMetadata).toEqual({
+      source: sourceExtDir,
+      type: 'link',
+    });
+    expect(linkedExt.contextFiles).toEqual([
+      path.join(sourceExtDir, 'context.md'),
+    ]);
+  });
+
+  it('should resolve environment variables in extension configuration', () => {
+    process.env.TEST_API_KEY = 'test-api-key-123';
+    process.env.TEST_DB_URL = 'postgresql://localhost:5432/testdb';
+
+    try {
+      const userExtensionsDir = path.join(
+        tempHomeDir,
+        EXTENSIONS_DIRECTORY_NAME,
+      );
+      fs.mkdirSync(userExtensionsDir, { recursive: true });
+
+      const extDir = path.join(userExtensionsDir, 'test-extension');
+      fs.mkdirSync(extDir);
+
+      // Write config to a separate file for clarity and good practices
+      const configPath = path.join(extDir, EXTENSIONS_CONFIG_FILENAME);
+      const extensionConfig = {
+        name: 'test-extension',
+        version: '1.0.0',
+        mcpServers: {
+          'test-server': {
+            command: 'node',
+            args: ['server.js'],
+            env: {
+              API_KEY: '$TEST_API_KEY',
+              DATABASE_URL: '${TEST_DB_URL}',
+              STATIC_VALUE: 'no-substitution',
+            },
+          },
+        },
+      };
+      fs.writeFileSync(configPath, JSON.stringify(extensionConfig));
+
+      const extensions = loadExtensions();
+
+      expect(extensions).toHaveLength(1);
+      const extension = extensions[0];
+      expect(extension.config.name).toBe('test-extension');
+      expect(extension.config.mcpServers).toBeDefined();
+
+      const serverConfig = extension.config.mcpServers?.['test-server'];
+      expect(serverConfig).toBeDefined();
+      expect(serverConfig?.env).toBeDefined();
+      expect(serverConfig?.env?.API_KEY).toBe('test-api-key-123');
+      expect(serverConfig?.env?.DATABASE_URL).toBe(
+        'postgresql://localhost:5432/testdb',
+      );
+      expect(serverConfig?.env?.STATIC_VALUE).toBe('no-substitution');
+    } finally {
+      delete process.env.TEST_API_KEY;
+      delete process.env.TEST_DB_URL;
+    }
+  });
+
+  it('should handle missing environment variables gracefully', () => {
+    const userExtensionsDir = path.join(tempHomeDir, EXTENSIONS_DIRECTORY_NAME);
+    fs.mkdirSync(userExtensionsDir, { recursive: true });
+
+    const extDir = path.join(userExtensionsDir, 'test-extension');
+    fs.mkdirSync(extDir);
+
+    const extensionConfig = {
+      name: 'test-extension',
+      version: '1.0.0',
+      mcpServers: {
+        'test-server': {
+          command: 'node',
+          args: ['server.js'],
+          env: {
+            MISSING_VAR: '$UNDEFINED_ENV_VAR',
+            MISSING_VAR_BRACES: '${ALSO_UNDEFINED}',
+          },
+        },
+      },
+    };
+
+    fs.writeFileSync(
+      path.join(extDir, EXTENSIONS_CONFIG_FILENAME),
+      JSON.stringify(extensionConfig),
+    );
+
+    const extensions = loadExtensions();
+
+    expect(extensions).toHaveLength(1);
+    const extension = extensions[0];
+    const serverConfig = extension.config.mcpServers!['test-server'];
+    expect(serverConfig.env).toBeDefined();
+    expect(serverConfig.env!.MISSING_VAR).toBe('$UNDEFINED_ENV_VAR');
+    expect(serverConfig.env!.MISSING_VAR_BRACES).toBe('${ALSO_UNDEFINED}');
+  });
 });
 
 describe('annotateActiveExtensions', () => {
-  const extensions = [
+  const extensions: Extension[] = [
     {
       path: '/path/to/ext1',
       config: { name: 'ext1', version: '1.0.0' },
@@ -283,24 +422,25 @@ describe('installExtension', () => {
       path.join(os.tmpdir(), 'gemini-cli-test-home-'),
     );
     vi.mocked(os.homedir).mockReturnValue(tempHomeDir);
-    userExtensionsDir = path.join(tempHomeDir, '.gemini', 'extensions');
+    userExtensionsDir = path.join(tempHomeDir, GEMINI_DIR, 'extensions');
     // Clean up before each test
     fs.rmSync(userExtensionsDir, { recursive: true, force: true });
     fs.mkdirSync(userExtensionsDir, { recursive: true });
-
+    vi.mocked(isWorkspaceTrusted).mockReturnValue(true);
     vi.mocked(execSync).mockClear();
   });
 
   afterEach(() => {
     fs.rmSync(tempHomeDir, { recursive: true, force: true });
+    fs.rmSync(userExtensionsDir, { recursive: true, force: true });
   });
 
   it('should install an extension from a local path', async () => {
-    const sourceExtDir = createExtension(
-      tempHomeDir,
-      'my-local-extension',
-      '1.0.0',
-    );
+    const sourceExtDir = createExtension({
+      extensionsDir: tempHomeDir,
+      name: 'my-local-extension',
+      version: '1.0.0',
+    });
     const targetExtDir = path.join(userExtensionsDir, 'my-local-extension');
     const metadataPath = path.join(targetExtDir, INSTALL_METADATA_FILENAME);
 
@@ -317,11 +457,11 @@ describe('installExtension', () => {
   });
 
   it('should throw an error if the extension already exists', async () => {
-    const sourceExtDir = createExtension(
-      tempHomeDir,
-      'my-local-extension',
-      '1.0.0',
-    );
+    const sourceExtDir = createExtension({
+      extensionsDir: tempHomeDir,
+      name: 'my-local-extension',
+      version: '1.0.0',
+    });
     await installExtension({ source: sourceExtDir, type: 'local' });
     await expect(
       installExtension({ source: sourceExtDir, type: 'local' }),
@@ -372,6 +512,44 @@ describe('installExtension', () => {
     });
     fs.rmSync(targetExtDir, { recursive: true, force: true });
   });
+
+  it('should install a linked extension', async () => {
+    const sourceExtDir = createExtension({
+      extensionsDir: tempHomeDir,
+      name: 'my-linked-extension',
+      version: '1.0.0',
+    });
+    const targetExtDir = path.join(userExtensionsDir, 'my-linked-extension');
+    const metadataPath = path.join(targetExtDir, INSTALL_METADATA_FILENAME);
+    const configPath = path.join(targetExtDir, EXTENSIONS_CONFIG_FILENAME);
+
+    await installExtension({ source: sourceExtDir, type: 'link' });
+
+    expect(fs.existsSync(targetExtDir)).toBe(true);
+    expect(fs.existsSync(metadataPath)).toBe(true);
+
+    expect(fs.existsSync(configPath)).toBe(false);
+
+    const metadata = JSON.parse(fs.readFileSync(metadataPath, 'utf-8'));
+    expect(metadata).toEqual({
+      source: sourceExtDir,
+      type: 'link',
+    });
+    fs.rmSync(targetExtDir, { recursive: true, force: true });
+  });
+
+  it('should log to clearcut on successful install', async () => {
+    const sourceExtDir = createExtension({
+      extensionsDir: tempHomeDir,
+      name: 'my-local-extension',
+      version: '1.0.0',
+    });
+
+    await installExtension({ source: sourceExtDir, type: 'local' });
+
+    const logger = ClearcutLogger.getInstance({} as Config);
+    expect(logger?.logExtensionInstallEvent).toHaveBeenCalled();
+  });
 });
 
 describe('uninstallExtension', () => {
@@ -383,7 +561,7 @@ describe('uninstallExtension', () => {
       path.join(os.tmpdir(), 'gemini-cli-test-home-'),
     );
     vi.mocked(os.homedir).mockReturnValue(tempHomeDir);
-    userExtensionsDir = path.join(tempHomeDir, '.gemini', 'extensions');
+    userExtensionsDir = path.join(tempHomeDir, GEMINI_DIR, 'extensions');
     // Clean up before each test
     fs.rmSync(userExtensionsDir, { recursive: true, force: true });
     fs.mkdirSync(userExtensionsDir, { recursive: true });
@@ -396,11 +574,11 @@ describe('uninstallExtension', () => {
   });
 
   it('should uninstall an extension by name', async () => {
-    const sourceExtDir = createExtension(
-      userExtensionsDir,
-      'my-local-extension',
-      '1.0.0',
-    );
+    const sourceExtDir = createExtension({
+      extensionsDir: userExtensionsDir,
+      name: 'my-local-extension',
+      version: '1.0.0',
+    });
 
     await uninstallExtension('my-local-extension');
 
@@ -408,21 +586,21 @@ describe('uninstallExtension', () => {
   });
 
   it('should uninstall an extension by name and retain existing extensions', async () => {
-    const sourceExtDir = createExtension(
-      userExtensionsDir,
-      'my-local-extension',
-      '1.0.0',
-    );
-    const otherExtDir = createExtension(
-      userExtensionsDir,
-      'other-extension',
-      '1.0.0',
-    );
+    const sourceExtDir = createExtension({
+      extensionsDir: userExtensionsDir,
+      name: 'my-local-extension',
+      version: '1.0.0',
+    });
+    const otherExtDir = createExtension({
+      extensionsDir: userExtensionsDir,
+      name: 'other-extension',
+      version: '1.0.0',
+    });
 
     await uninstallExtension('my-local-extension');
 
     expect(fs.existsSync(sourceExtDir)).toBe(false);
-    expect(loadExtensions(tempHomeDir)).toHaveLength(1);
+    expect(loadExtensions()).toHaveLength(1);
     expect(fs.existsSync(otherExtDir)).toBe(true);
   });
 
@@ -436,6 +614,7 @@ describe('uninstallExtension', () => {
 describe('performWorkspaceExtensionMigration', () => {
   let tempWorkspaceDir: string;
   let tempHomeDir: string;
+  let workspaceExtensionsDir: string;
 
   beforeEach(() => {
     tempWorkspaceDir = fs.mkdtempSync(
@@ -445,6 +624,13 @@ describe('performWorkspaceExtensionMigration', () => {
       path.join(os.tmpdir(), 'gemini-cli-test-home-'),
     );
     vi.mocked(os.homedir).mockReturnValue(tempHomeDir);
+    vi.mocked(isWorkspaceTrusted).mockReturnValue(true);
+
+    workspaceExtensionsDir = path.join(
+      tempWorkspaceDir,
+      EXTENSIONS_DIRECTORY_NAME,
+    );
+    fs.mkdirSync(workspaceExtensionsDir, { recursive: true });
   });
 
   afterEach(() => {
@@ -453,15 +639,68 @@ describe('performWorkspaceExtensionMigration', () => {
     vi.restoreAllMocks();
   });
 
+  describe('folder trust', () => {
+    it('refuses to install extensions from untrusted folders', async () => {
+      vi.mocked(isWorkspaceTrusted).mockReturnValue(false);
+      const ext1Path = createExtension({
+        extensionsDir: workspaceExtensionsDir,
+        name: 'ext1',
+        version: '1.0.0',
+      });
+
+      const failed = await performWorkspaceExtensionMigration([
+        loadExtension(ext1Path)!,
+      ]);
+
+      expect(failed).toEqual(['ext1']);
+    });
+
+    it('does not copy extensions to the user dir', async () => {
+      vi.mocked(isWorkspaceTrusted).mockReturnValue(false);
+      const ext1Path = createExtension({
+        extensionsDir: workspaceExtensionsDir,
+        name: 'ext1',
+        version: '1.0.0',
+      });
+
+      await performWorkspaceExtensionMigration([loadExtension(ext1Path)!]);
+
+      const userExtensionsDir = path.join(
+        tempHomeDir,
+        GEMINI_DIR,
+        'extensions',
+      );
+
+      expect(() => fs.readdirSync(userExtensionsDir)).toThrow();
+    });
+
+    it('does not load any extensions in the workspace config', async () => {
+      vi.mocked(isWorkspaceTrusted).mockReturnValue(false);
+      const ext1Path = createExtension({
+        extensionsDir: workspaceExtensionsDir,
+        name: 'ext1',
+        version: '1.0.0',
+      });
+
+      await performWorkspaceExtensionMigration([loadExtension(ext1Path)!]);
+      const extensions = loadExtensions();
+
+      expect(extensions).toEqual([]);
+    });
+  });
+
   it('should install the extensions in the user directory', async () => {
-    const workspaceExtensionsDir = path.join(
-      tempWorkspaceDir,
-      EXTENSIONS_DIRECTORY_NAME,
-    );
-    fs.mkdirSync(workspaceExtensionsDir, { recursive: true });
-    const ext1Path = createExtension(workspaceExtensionsDir, 'ext1', '1.0.0');
-    const ext2Path = createExtension(workspaceExtensionsDir, 'ext2', '1.0.0');
-    const extensionsToMigrate = [
+    const ext1Path = createExtension({
+      extensionsDir: workspaceExtensionsDir,
+      name: 'ext1',
+      version: '1.0.0',
+    });
+    const ext2Path = createExtension({
+      extensionsDir: workspaceExtensionsDir,
+      name: 'ext2',
+      version: '1.0.0',
+    });
+    const extensionsToMigrate: Extension[] = [
       loadExtension(ext1Path)!,
       loadExtension(ext2Path)!,
     ];
@@ -470,9 +709,9 @@ describe('performWorkspaceExtensionMigration', () => {
 
     expect(failed).toEqual([]);
 
-    const userExtensionsDir = path.join(tempHomeDir, '.gemini', 'extensions');
+    const userExtensionsDir = path.join(tempHomeDir, GEMINI_DIR, 'extensions');
     const userExt1Path = path.join(userExtensionsDir, 'ext1');
-    const extensions = loadExtensions(tempWorkspaceDir);
+    const extensions = loadExtensions();
 
     expect(extensions).toHaveLength(2);
     const metadataPath = path.join(userExt1Path, INSTALL_METADATA_FILENAME);
@@ -485,15 +724,13 @@ describe('performWorkspaceExtensionMigration', () => {
   });
 
   it('should return the names of failed installations', async () => {
-    const workspaceExtensionsDir = path.join(
-      tempWorkspaceDir,
-      EXTENSIONS_DIRECTORY_NAME,
-    );
-    fs.mkdirSync(workspaceExtensionsDir, { recursive: true });
+    const ext1Path = createExtension({
+      extensionsDir: workspaceExtensionsDir,
+      name: 'ext1',
+      version: '1.0.0',
+    });
 
-    const ext1Path = createExtension(workspaceExtensionsDir, 'ext1', '1.0.0');
-
-    const extensions = [
+    const extensions: Extension[] = [
       loadExtension(ext1Path)!,
       {
         path: '/ext/path/1',
@@ -507,14 +744,14 @@ describe('performWorkspaceExtensionMigration', () => {
   });
 });
 
-function createExtension(
-  extensionsDir: string,
-  name: string,
-  version: string,
+function createExtension({
+  extensionsDir = 'extensions-dir',
+  name = 'my-extension',
+  version = '1.0.0',
   addContextFile = false,
-  contextFileName?: string,
-  mcpServers?: Record<string, MCPServerConfig>,
-): string {
+  contextFileName = undefined as string | undefined,
+  mcpServers = {} as Record<string, MCPServerConfig>,
+} = {}): string {
   const extDir = path.join(extensionsDir, name);
   fs.mkdirSync(extDir, { recursive: true });
   fs.writeFileSync(
@@ -527,7 +764,9 @@ function createExtension(
   }
 
   if (contextFileName) {
-    fs.writeFileSync(path.join(extDir, contextFileName), 'context');
+    const contextPath = path.join(extDir, contextFileName);
+    fs.mkdirSync(path.dirname(contextPath), { recursive: true });
+    fs.writeFileSync(contextPath, 'context');
   }
   return extDir;
 }
@@ -541,10 +780,11 @@ describe('updateExtension', () => {
       path.join(os.tmpdir(), 'gemini-cli-test-home-'),
     );
     vi.mocked(os.homedir).mockReturnValue(tempHomeDir);
-    userExtensionsDir = path.join(tempHomeDir, '.gemini', 'extensions');
+    userExtensionsDir = path.join(tempHomeDir, GEMINI_DIR, 'extensions');
     // Clean up before each test
     fs.rmSync(userExtensionsDir, { recursive: true, force: true });
     fs.mkdirSync(userExtensionsDir, { recursive: true });
+    vi.mocked(isWorkspaceTrusted).mockReturnValue(true);
 
     vi.mocked(execSync).mockClear();
   });
@@ -554,13 +794,11 @@ describe('updateExtension', () => {
   });
 
   it('should update a git-installed extension', async () => {
-    // 1. "Install" an extension
     const gitUrl = 'https://github.com/google/gemini-extensions.git';
     const extensionName = 'gemini-extensions';
     const targetExtDir = path.join(userExtensionsDir, extensionName);
     const metadataPath = path.join(targetExtDir, INSTALL_METADATA_FILENAME);
 
-    // Create the "installed" extension directory and files
     fs.mkdirSync(targetExtDir, { recursive: true });
     fs.writeFileSync(
       path.join(targetExtDir, EXTENSIONS_CONFIG_FILENAME),
@@ -571,10 +809,8 @@ describe('updateExtension', () => {
       JSON.stringify({ source: gitUrl, type: 'git' }),
     );
 
-    // 2. Mock the git clone for the update
     const clone = vi.fn().mockImplementation(async (_, destination) => {
       fs.mkdirSync(destination, { recursive: true });
-      // This is the "updated" version
       fs.writeFileSync(
         path.join(destination, EXTENSIONS_CONFIG_FILENAME),
         JSON.stringify({ name: extensionName, version: '1.1.0' }),
@@ -586,16 +822,14 @@ describe('updateExtension', () => {
       clone,
     } as unknown as SimpleGit);
 
-    // 3. Call updateExtension
-    const updateInfo = await updateExtension(extensionName);
+    const updateInfo = await updateExtension(loadExtension(targetExtDir));
 
-    // 4. Assertions
     expect(updateInfo).toEqual({
+      name: 'gemini-extensions',
       originalVersion: '1.0.0',
       updatedVersion: '1.1.0',
     });
 
-    // Check that the config file reflects the new version
     const updatedConfig = JSON.parse(
       fs.readFileSync(
         path.join(targetExtDir, EXTENSIONS_CONFIG_FILENAME),
@@ -670,7 +904,7 @@ describe('enableExtension', () => {
     tempHomeDir = fs.mkdtempSync(
       path.join(os.tmpdir(), 'gemini-cli-test-home-'),
     );
-    userExtensionsDir = path.join(tempHomeDir, '.gemini', 'extensions');
+    userExtensionsDir = path.join(tempHomeDir, GEMINI_DIR, 'extensions');
     vi.mocked(os.homedir).mockReturnValue(tempHomeDir);
     vi.spyOn(process, 'cwd').mockReturnValue(tempWorkspaceDir);
   });
@@ -686,7 +920,7 @@ describe('enableExtension', () => {
   });
 
   const getActiveExtensions = (): GeminiCLIExtension[] => {
-    const extensions = loadExtensions(tempWorkspaceDir);
+    const extensions = loadExtensions();
     const activeExtensions = annotateActiveExtensions(
       extensions,
       [],
@@ -696,7 +930,11 @@ describe('enableExtension', () => {
   };
 
   it('should enable an extension at the user scope', () => {
-    createExtension(userExtensionsDir, 'ext1', '1.0.0');
+    createExtension({
+      extensionsDir: userExtensionsDir,
+      name: 'ext1',
+      version: '1.0.0',
+    });
     disableExtension('ext1', SettingScope.User);
     let activeExtensions = getActiveExtensions();
     expect(activeExtensions).toHaveLength(0);
@@ -708,7 +946,11 @@ describe('enableExtension', () => {
   });
 
   it('should enable an extension at the workspace scope', () => {
-    createExtension(userExtensionsDir, 'ext1', '1.0.0');
+    createExtension({
+      extensionsDir: userExtensionsDir,
+      name: 'ext1',
+      version: '1.0.0',
+    });
     disableExtension('ext1', SettingScope.Workspace);
     let activeExtensions = getActiveExtensions();
     expect(activeExtensions).toHaveLength(0);

packages/cli/src/config/extension.ts

@@ -8,7 +8,13 @@ import type {
   MCPServerConfig,
   GeminiCLIExtension,
 } from '@google/gemini-cli-core';
-import { Storage } from '@google/gemini-cli-core';
+import {
+  GEMINI_DIR,
+  Storage,
+  ClearcutLogger,
+  Config,
+  ExtensionInstallEvent,
+} from '@google/gemini-cli-core';
 import * as fs from 'node:fs';
 import * as path from 'node:path';
 import * as os from 'node:os';
@@ -16,8 +22,11 @@ import { simpleGit } from 'simple-git';
 import { SettingScope, loadSettings } from '../config/settings.js';
 import { getErrorMessage } from '../utils/errors.js';
 import { recursivelyHydrateStrings } from './extensions/variables.js';
+import { isWorkspaceTrusted } from './trustedFolders.js';
+import { resolveEnvVarsInObject } from '../utils/envVarResolver.js';
+import { randomUUID } from 'node:crypto';
 
-export const EXTENSIONS_DIRECTORY_NAME = '.gemini/extensions';
+export const EXTENSIONS_DIRECTORY_NAME = path.join(GEMINI_DIR, 'extensions');
 
 export const EXTENSIONS_CONFIG_FILENAME = 'gemini-extension.json';
 export const INSTALL_METADATA_FILENAME = '.gemini-extension-install.json';
@@ -39,10 +48,11 @@ export interface ExtensionConfig {
 
 export interface ExtensionInstallMetadata {
   source: string;
-  type: 'git' | 'local';
+  type: 'git' | 'local' | 'link';
 }
 
 export interface ExtensionUpdateInfo {
+  name: string;
   originalVersion: string;
   updatedVersion: string;
 }
@@ -78,6 +88,10 @@ export class ExtensionStorage {
 }
 
 export function getWorkspaceExtensions(workspaceDir: string): Extension[] {
+  // If the workspace dir is the user extensions dir, there are no workspace extensions.
+  if (path.resolve(workspaceDir) === path.resolve(os.homedir())) {
+    return [];
+  }
   return loadExtensionsFromDir(workspaceDir);
 }
 
@@ -107,12 +121,18 @@ export async function performWorkspaceExtensionMigration(
   return failedInstallNames;
 }
 
-export function loadExtensions(workspaceDir: string): Extension[] {
+export function loadExtensions(
+  workspaceDir: string = process.cwd(),
+): Extension[] {
   const settings = loadSettings(workspaceDir).merged;
   const disabledExtensions = settings.extensions?.disabled ?? [];
   const allExtensions = [...loadUserExtensions()];
 
-  if (!settings.experimental?.extensionManagement) {
+  if (
+    (isWorkspaceTrusted(settings) ?? true) &&
+    // Default management setting to true
+    !(settings.experimental?.extensionManagement ?? true)
+  ) {
     allExtensions.push(...getWorkspaceExtensions(workspaceDir));
   }
 
@@ -169,17 +189,27 @@ export function loadExtension(extensionDir: string): Extension | null {
     return null;
   }
 
-  const configFilePath = path.join(extensionDir, EXTENSIONS_CONFIG_FILENAME);
+  const installMetadata = loadInstallMetadata(extensionDir);
+  let effectiveExtensionPath = extensionDir;
+
+  if (installMetadata?.type === 'link') {
+    effectiveExtensionPath = installMetadata.source;
+  }
+
+  const configFilePath = path.join(
+    effectiveExtensionPath,
+    EXTENSIONS_CONFIG_FILENAME,
+  );
   if (!fs.existsSync(configFilePath)) {
     console.error(
-      `Warning: extension directory ${extensionDir} does not contain a config file ${configFilePath}.`,
+      `Warning: extension directory ${effectiveExtensionPath} does not contain a config file ${configFilePath}.`,
     );
     return null;
   }
 
   try {
     const configContent = fs.readFileSync(configFilePath, 'utf-8');
-    const config = recursivelyHydrateStrings(JSON.parse(configContent), {
+    let config = recursivelyHydrateStrings(JSON.parse(configContent), {
       extensionPath: extensionDir,
       '/': path.sep,
       pathSeparator: path.sep,
@@ -191,15 +221,19 @@ export function loadExtension(extensionDir: string): Extension | null {
       return null;
     }
 
+    config = resolveEnvVarsInObject(config);
+
     const contextFiles = getContextFileNames(config)
-      .map((contextFileName) => path.join(extensionDir, contextFileName))
+      .map((contextFileName) =>
+        path.join(effectiveExtensionPath, contextFileName),
+      )
       .filter((contextFilePath) => fs.existsSync(contextFilePath));
 
     return {
-      path: extensionDir,
+      path: effectiveExtensionPath,
       config,
       contextFiles,
-      installMetadata: loadInstallMetadata(extensionDir),
+      installMetadata,
     };
   } catch (e) {
     console.error(
@@ -323,63 +357,140 @@ export async function installExtension(
   installMetadata: ExtensionInstallMetadata,
   cwd: string = process.cwd(),
 ): Promise<string> {
-  const extensionsDir = ExtensionStorage.getUserExtensionsDir();
-  await fs.promises.mkdir(extensionsDir, { recursive: true });
+  const config = new Config({
+    sessionId: randomUUID(),
+    targetDir: process.cwd(),
+    cwd: process.cwd(),
+    model: '',
+    debugMode: false,
+  });
+  const logger = ClearcutLogger.getInstance(config);
+  let newExtensionConfig: ExtensionConfig | null = null;
+  let localSourcePath: string | undefined;
 
-  // Convert relative paths to absolute paths for the metadata file.
-  if (
-    installMetadata.type === 'local' &&
-    !path.isAbsolute(installMetadata.source)
-  ) {
-    installMetadata.source = path.resolve(cwd, installMetadata.source);
-  }
-
-  let localSourcePath: string;
-  let tempDir: string | undefined;
-  if (installMetadata.type === 'git') {
-    tempDir = await ExtensionStorage.createTmpDir();
-    await cloneFromGit(installMetadata.source, tempDir);
-    localSourcePath = tempDir;
-  } else {
-    localSourcePath = installMetadata.source;
-  }
-  let newExtensionName: string | undefined;
   try {
-    const newExtension = loadExtension(localSourcePath);
-    if (!newExtension) {
+    const settings = loadSettings(cwd).merged;
+    if (!isWorkspaceTrusted(settings)) {
       throw new Error(
-        `Invalid extension at ${installMetadata.source}. Please make sure it has a valid gemini-extension.json file.`,
+        `Could not install extension from untrusted folder at ${installMetadata.source}`,
       );
     }
 
-    // ~/.gemini/extensions/{ExtensionConfig.name}.
-    newExtensionName = newExtension.config.name;
-    const extensionStorage = new ExtensionStorage(newExtensionName);
-    const destinationPath = extensionStorage.getExtensionDir();
+    const extensionsDir = ExtensionStorage.getUserExtensionsDir();
+    await fs.promises.mkdir(extensionsDir, { recursive: true });
 
-    const installedExtensions = loadUserExtensions();
     if (
-      installedExtensions.some(
-        (installed) => installed.config.name === newExtensionName,
-      )
+      !path.isAbsolute(installMetadata.source) &&
+      (installMetadata.type === 'local' || installMetadata.type === 'link')
     ) {
-      throw new Error(
-        `Extension "${newExtensionName}" is already installed. Please uninstall it first.`,
+      installMetadata.source = path.resolve(cwd, installMetadata.source);
+    }
+
+    let tempDir: string | undefined;
+
+    if (installMetadata.type === 'git') {
+      tempDir = await ExtensionStorage.createTmpDir();
+      await cloneFromGit(installMetadata.source, tempDir);
+      localSourcePath = tempDir;
+    } else if (
+      installMetadata.type === 'local' ||
+      installMetadata.type === 'link'
+    ) {
+      localSourcePath = installMetadata.source;
+    } else {
+      throw new Error(`Unsupported install type: ${installMetadata.type}`);
+    }
+
+    try {
+      newExtensionConfig = await loadExtensionConfig(localSourcePath);
+      if (!newExtensionConfig) {
+        throw new Error(
+          `Invalid extension at ${installMetadata.source}. Please make sure it has a valid gemini-extension.json file.`,
+        );
+      }
+
+      const newExtensionName = newExtensionConfig.name;
+      const extensionStorage = new ExtensionStorage(newExtensionName);
+      const destinationPath = extensionStorage.getExtensionDir();
+
+      const installedExtensions = loadUserExtensions();
+      if (
+        installedExtensions.some(
+          (installed) => installed.config.name === newExtensionName,
+        )
+      ) {
+        throw new Error(
+          `Extension "${newExtensionName}" is already installed. Please uninstall it first.`,
+        );
+      }
+
+      await fs.promises.mkdir(destinationPath, { recursive: true });
+
+      if (installMetadata.type === 'local' || installMetadata.type === 'git') {
+        await copyExtension(localSourcePath, destinationPath);
+      }
+
+      const metadataString = JSON.stringify(installMetadata, null, 2);
+      const metadataPath = path.join(
+        destinationPath,
+        INSTALL_METADATA_FILENAME,
       );
+      await fs.promises.writeFile(metadataPath, metadataString);
+    } finally {
+      if (tempDir) {
+        await fs.promises.rm(tempDir, { recursive: true, force: true });
+      }
     }
 
-    await copyExtension(localSourcePath, destinationPath);
+    logger?.logExtensionInstallEvent(
+      new ExtensionInstallEvent(
+        newExtensionConfig!.name,
+        newExtensionConfig!.version,
+        installMetadata.source,
+        'success',
+      ),
+    );
 
-    const metadataString = JSON.stringify(installMetadata, null, 2);
-    const metadataPath = path.join(destinationPath, INSTALL_METADATA_FILENAME);
-    await fs.promises.writeFile(metadataPath, metadataString);
-  } finally {
-    if (tempDir) {
-      await fs.promises.rm(tempDir, { recursive: true, force: true });
+    return newExtensionConfig!.name;
+  } catch (error) {
+    // Attempt to load config from the source path even if installation fails
+    // to get the name and version for logging.
+    if (!newExtensionConfig && localSourcePath) {
+      newExtensionConfig = await loadExtensionConfig(localSourcePath);
     }
+    logger?.logExtensionInstallEvent(
+      new ExtensionInstallEvent(
+        newExtensionConfig?.name ?? '',
+        newExtensionConfig?.version ?? '',
+        installMetadata.source,
+        'error',
+      ),
+    );
+    throw error;
   }
+}
 
-  return newExtensionName;
+export async function loadExtensionConfig(
+  extensionDir: string,
+): Promise<ExtensionConfig | null> {
+  const configFilePath = path.join(extensionDir, EXTENSIONS_CONFIG_FILENAME);
+  if (!fs.existsSync(configFilePath)) {
+    return null;
+  }
+  try {
+    const configContent = fs.readFileSync(configFilePath, 'utf-8');
+    const config = recursivelyHydrateStrings(JSON.parse(configContent), {
+      extensionPath: extensionDir,
+      '/': path.sep,
+      pathSeparator: path.sep,
+    }) as unknown as ExtensionConfig;
+    if (!config.name || !config.version) {
+      return null;
+    }
+    return config;
+  } catch (_) {
+    return null;
+  }
 }
 
 export async function uninstallExtension(
@@ -410,7 +521,7 @@ export function toOutputString(extension: Extension): string {
   let output = `${extension.config.name} (${extension.config.version})`;
   output += `\n Path: ${extension.path}`;
   if (extension.installMetadata) {
-    output += `\n Source: ${extension.installMetadata.source}`;
+    output += `\n Source: ${extension.installMetadata.source} (Type: ${extension.installMetadata.type})`;
   }
   if (extension.contextFiles.length > 0) {
     output += `\n Context files:`;
@@ -433,10 +544,10 @@ export function toOutputString(extension: Extension): string {
   return output;
 }
 
-export async function updateExtension(
+export async function updateExtensionByName(
   extensionName: string,
   cwd: string = process.cwd(),
-): Promise<ExtensionUpdateInfo | undefined> {
+): Promise<ExtensionUpdateInfo> {
   const installedExtensions = loadUserExtensions();
   const extension = installedExtensions.find(
     (installed) => installed.config.name === extensionName,
@@ -446,24 +557,37 @@ export async function updateExtension(
       `Extension "${extensionName}" not found. Run gemini extensions list to see available extensions.`,
     );
   }
+  return await updateExtension(extension, cwd);
+}
+
+export async function updateExtension(
+  extension: Extension,
+  cwd: string = process.cwd(),
+): Promise<ExtensionUpdateInfo> {
   if (!extension.installMetadata) {
-    throw new Error(
-      `Extension cannot be updated because it is missing the .gemini-extension.install.json file. To update manually, uninstall and then reinstall the updated version.`,
-    );
+    throw new Error(`Extension ${extension.config.name} cannot be updated.`);
+  }
+  if (extension.installMetadata.type === 'link') {
+    throw new Error(`Extension is linked so does not need to be updated`);
   }
   const originalVersion = extension.config.version;
+
   const tempDir = await ExtensionStorage.createTmpDir();
   try {
     await copyExtension(extension.path, tempDir);
-    await uninstallExtension(extensionName, cwd);
+    await uninstallExtension(extension.config.name, cwd);
     await installExtension(extension.installMetadata, cwd);
 
-    const updatedExtension = loadExtension(extension.path);
+    const updatedExtensionStorage = new ExtensionStorage(extension.config.name);
+    const updatedExtension = loadExtension(
+      updatedExtensionStorage.getExtensionDir(),
+    );
     if (!updatedExtension) {
       throw new Error('Updated extension not found after installation.');
     }
     const updatedVersion = updatedExtension.config.version;
     return {
+      name: extension.config.name,
       originalVersion,
       updatedVersion,
     };
@@ -526,3 +650,14 @@ function removeFromDisabledExtensions(
     settings.setValue(scope, 'extensions', extensionSettings);
   }
 }
+
+export async function updateAllUpdatableExtensions(
+  cwd: string = process.cwd(),
+): Promise<ExtensionUpdateInfo[]> {
+  const extensions = loadExtensions(cwd).filter(
+    (extension) => !!extension.installMetadata,
+  );
+  return await Promise.all(
+    extensions.map((extension) => updateExtension(extension, cwd)),
+  );
+}

packages/cli/src/config/keyBindings.ts

@@ -20,6 +20,7 @@ export enum Command {
   KILL_LINE_RIGHT = 'killLineRight',
   KILL_LINE_LEFT = 'killLineLeft',
   CLEAR_INPUT = 'clearInput',
+  DELETE_WORD_BACKWARD = 'deleteWordBackward',
 
   // Screen control
   CLEAR_SCREEN = 'clearScreen',
@@ -89,46 +90,38 @@ export type KeyBindingConfig = {
 export const defaultKeyBindings: KeyBindingConfig = {
   // Basic bindings
   [Command.RETURN]: [{ key: 'return' }],
-  // Original: key.name === 'escape'
   [Command.ESCAPE]: [{ key: 'escape' }],
 
   // Cursor movement
-  // Original: key.ctrl && key.name === 'a'
   [Command.HOME]: [{ key: 'a', ctrl: true }],
-  // Original: key.ctrl && key.name === 'e'
   [Command.END]: [{ key: 'e', ctrl: true }],
 
   // Text deletion
-  // Original: key.ctrl && key.name === 'k'
   [Command.KILL_LINE_RIGHT]: [{ key: 'k', ctrl: true }],
-  // Original: key.ctrl && key.name === 'u'
   [Command.KILL_LINE_LEFT]: [{ key: 'u', ctrl: true }],
-  // Original: key.ctrl && key.name === 'c'
   [Command.CLEAR_INPUT]: [{ key: 'c', ctrl: true }],
+  // Added command (meta/alt/option) for mac compatibility
+  [Command.DELETE_WORD_BACKWARD]: [
+    { key: 'backspace', ctrl: true },
+    { key: 'backspace', command: true },
+  ],
 
   // Screen control
-  // Original: key.ctrl && key.name === 'l'
   [Command.CLEAR_SCREEN]: [{ key: 'l', ctrl: true }],
 
   // History navigation
-  // Original: key.ctrl && key.name === 'p'
   [Command.HISTORY_UP]: [{ key: 'p', ctrl: true }],
-  // Original: key.ctrl && key.name === 'n'
   [Command.HISTORY_DOWN]: [{ key: 'n', ctrl: true }],
-  // Original: key.name === 'up'
   [Command.NAVIGATION_UP]: [{ key: 'up' }],
-  // Original: key.name === 'down'
   [Command.NAVIGATION_DOWN]: [{ key: 'down' }],
 
   // Auto-completion
-  // Original: key.name === 'tab' || (key.name === 'return' && !key.ctrl)
   [Command.ACCEPT_SUGGESTION]: [{ key: 'tab' }, { key: 'return', ctrl: false }],
   // Completion navigation (arrow or Ctrl+P/N)
   [Command.COMPLETION_UP]: [{ key: 'up' }, { key: 'p', ctrl: true }],
   [Command.COMPLETION_DOWN]: [{ key: 'down' }, { key: 'n', ctrl: true }],
 
   // Text input
-  // Original: key.name === 'return' && !key.ctrl && !key.meta && !key.paste
   // Must also exclude shift to allow shift+enter for newline
   [Command.SUBMIT]: [
     {
@@ -139,7 +132,6 @@ export const defaultKeyBindings: KeyBindingConfig = {
       shift: false,
     },
   ],
-  // Original: key.name === 'return' && (key.ctrl || key.meta || key.paste)
   // Split into multiple data-driven bindings
   // Now also includes shift+enter for multi-line input
   [Command.NEWLINE]: [
@@ -151,34 +143,23 @@ export const defaultKeyBindings: KeyBindingConfig = {
   ],
 
   // External tools
-  // Original: key.ctrl && (key.name === 'x' || key.sequence === '\x18')
   [Command.OPEN_EXTERNAL_EDITOR]: [
     { key: 'x', ctrl: true },
     { sequence: '\x18', ctrl: true },
   ],
-  // Original: key.ctrl && key.name === 'v'
   [Command.PASTE_CLIPBOARD_IMAGE]: [{ key: 'v', ctrl: true }],
 
   // App level bindings
-  // Original: key.ctrl && key.name === 'o'
   [Command.SHOW_ERROR_DETAILS]: [{ key: 'o', ctrl: true }],
-  // Original: key.ctrl && key.name === 't'
   [Command.TOGGLE_TOOL_DESCRIPTIONS]: [{ key: 't', ctrl: true }],
-  // Original: key.ctrl && key.name === 'g'
   [Command.TOGGLE_IDE_CONTEXT_DETAIL]: [{ key: 'g', ctrl: true }],
-  // Original: key.ctrl && (key.name === 'c' || key.name === 'C')
   [Command.QUIT]: [{ key: 'c', ctrl: true }],
-  // Original: key.ctrl && (key.name === 'd' || key.name === 'D')
   [Command.EXIT]: [{ key: 'd', ctrl: true }],
-  // Original: key.ctrl && key.name === 's'
   [Command.SHOW_MORE_LINES]: [{ key: 's', ctrl: true }],
 
   // Shell commands
-  // Original: key.ctrl && key.name === 'r'
   [Command.REVERSE_SEARCH]: [{ key: 'r', ctrl: true }],
-  // Original: key.name === 'return' && !key.ctrl
   // Note: original logic ONLY checked ctrl=false, ignored meta/shift/paste
   [Command.SUBMIT_REVERSE_SEARCH]: [{ key: 'return', ctrl: false }],
-  // Original: key.name === 'tab'
   [Command.ACCEPT_SUGGESTION_REVERSE_SEARCH]: [{ key: 'tab' }],
 };

packages/cli/src/config/settings.test.ts

@@ -34,7 +34,7 @@ vi.mock('./trustedFolders.js', () => ({
 }));
 
 // NOW import everything else, including the (now effectively re-exported) settings.js
-import * as pathActual from 'node:path'; // Restored for MOCK_WORKSPACE_SETTINGS_PATH
+import path, * as pathActual from 'node:path'; // Restored for MOCK_WORKSPACE_SETTINGS_PATH
 import {
   describe,
   it,
@@ -44,6 +44,7 @@ import {
   afterEach,
   type Mocked,
   type Mock,
+  fail,
 } from 'vitest';
 import * as fs from 'node:fs'; // fs will be mocked separately
 import stripJsonComments from 'strip-json-comments'; // Will be mocked separately
@@ -57,8 +58,11 @@ import {
   getSystemDefaultsPath,
   SETTINGS_DIRECTORY_NAME, // This is from the original module, but used by the mock.
   migrateSettingsToV1,
+  needsMigration,
   type Settings,
+  loadEnvironment,
 } from './settings.js';
+import { FatalConfigError, GEMINI_DIR } from '@google/gemini-cli-core';
 
 const MOCK_WORKSPACE_DIR = '/mock/workspace';
 // Use the (mocked) SETTINGS_DIRECTORY_NAME for consistency
@@ -122,33 +126,7 @@ describe('Settings Loading and Merging', () => {
       expect(settings.system.settings).toEqual({});
       expect(settings.user.settings).toEqual({});
       expect(settings.workspace.settings).toEqual({});
-      expect(settings.merged).toEqual({
-        ui: {
-          customThemes: {},
-        },
-        mcp: {},
-        mcpServers: {},
-        context: {
-          includeDirectories: [],
-        },
-        model: {
-          chatCompression: {},
-        },
-        advanced: {
-          excludedEnvVars: [],
-        },
-        extensions: {
-          disabled: [],
-          workspacesWithMigrationNudge: [],
-        },
-        security: {},
-        general: {},
-        privacy: {},
-        telemetry: {},
-        tools: {},
-        ide: {},
-      });
-      expect(settings.errors.length).toBe(0);
+      expect(settings.merged).toEqual({});
     });
 
     it('should load system settings if only system file exists', () => {
@@ -182,33 +160,6 @@ describe('Settings Loading and Merging', () => {
       expect(settings.workspace.settings).toEqual({});
       expect(settings.merged).toEqual({
         ...systemSettingsContent,
-        ui: {
-          ...systemSettingsContent.ui,
-          customThemes: {},
-        },
-        mcp: {},
-        mcpServers: {},
-        context: {
-          includeDirectories: [],
-        },
-        model: {
-          chatCompression: {},
-        },
-        advanced: {
-          excludedEnvVars: [],
-        },
-        extensions: {
-          disabled: [],
-          workspacesWithMigrationNudge: [],
-        },
-        security: {},
-        general: {},
-        privacy: {},
-        telemetry: {},
-        tools: {
-          sandbox: false,
-        },
-        ide: {},
       });
     });
 
@@ -244,32 +195,6 @@ describe('Settings Loading and Merging', () => {
       expect(settings.workspace.settings).toEqual({});
       expect(settings.merged).toEqual({
         ...userSettingsContent,
-        ui: {
-          ...userSettingsContent.ui,
-          customThemes: {},
-        },
-        mcp: {},
-        mcpServers: {},
-        context: {
-          ...userSettingsContent.context,
-          includeDirectories: [],
-        },
-        model: {
-          chatCompression: {},
-        },
-        advanced: {
-          excludedEnvVars: [],
-        },
-        extensions: {
-          disabled: [],
-          workspacesWithMigrationNudge: [],
-        },
-        security: {},
-        general: {},
-        privacy: {},
-        telemetry: {},
-        tools: {},
-        ide: {},
       });
     });
 
@@ -302,108 +227,17 @@ describe('Settings Loading and Merging', () => {
       expect(settings.user.settings).toEqual({});
       expect(settings.workspace.settings).toEqual(workspaceSettingsContent);
       expect(settings.merged).toEqual({
-        tools: {
-          sandbox: true,
-        },
-        context: {
-          fileName: 'WORKSPACE_CONTEXT.md',
-          includeDirectories: [],
-        },
-        ui: {
-          customThemes: {},
-        },
-        mcp: {},
-        mcpServers: {},
-        model: {
-          chatCompression: {},
-        },
-        advanced: {
-          excludedEnvVars: [],
-        },
-        extensions: {
-          disabled: [],
-          workspacesWithMigrationNudge: [],
-        },
-        security: {},
-        general: {},
-        privacy: {},
-        telemetry: {},
-        ide: {},
-      });
-    });
-
-    it('should merge user and workspace settings, with workspace taking precedence', () => {
-      (mockFsExistsSync as Mock).mockReturnValue(true);
-      const userSettingsContent = {
-        ui: {
-          theme: 'dark',
-        },
-        tools: {
-          sandbox: false,
-        },
-        context: {
-          fileName: 'USER_CONTEXT.md',
-        },
-      };
-      const workspaceSettingsContent = {
-        tools: {
-          sandbox: true,
-          core: ['tool1'],
-        },
-        context: {
-          fileName: 'WORKSPACE_CONTEXT.md',
-        },
-      };
-
-      (fs.readFileSync as Mock).mockImplementation(
-        (p: fs.PathOrFileDescriptor) => {
-          if (p === USER_SETTINGS_PATH)
-            return JSON.stringify(userSettingsContent);
-          if (p === MOCK_WORKSPACE_SETTINGS_PATH)
-            return JSON.stringify(workspaceSettingsContent);
-          return '';
-        },
-      );
-
-      const settings = loadSettings(MOCK_WORKSPACE_DIR);
-
-      expect(settings.user.settings).toEqual(userSettingsContent);
-      expect(settings.workspace.settings).toEqual(workspaceSettingsContent);
-      expect(settings.merged).toEqual({
-        ui: {
-          theme: 'dark',
-          customThemes: {},
-        },
-        tools: {
-          sandbox: true,
-          core: ['tool1'],
-        },
-        context: {
-          fileName: 'WORKSPACE_CONTEXT.md',
-          includeDirectories: [],
-        },
-        advanced: {
-          excludedEnvVars: [],
-        },
-        extensions: {
-          disabled: [],
-          workspacesWithMigrationNudge: [],
-        },
-        mcp: {},
-        mcpServers: {},
-        model: {
-          chatCompression: {},
-        },
-        security: {},
-        general: {},
-        privacy: {},
-        telemetry: {},
-        ide: {},
+        ...workspaceSettingsContent,
       });
     });
 
     it('should merge system, user and workspace settings, with system taking precedence over workspace, and workspace over user', () => {
-      (mockFsExistsSync as Mock).mockReturnValue(true);
+      (mockFsExistsSync as Mock).mockImplementation(
+        (p: fs.PathLike) =>
+          p === getSystemSettingsPath() ||
+          p === USER_SETTINGS_PATH ||
+          p === MOCK_WORKSPACE_SETTINGS_PATH,
+      );
       const systemSettingsContent = {
         ui: {
           theme: 'system-theme',
@@ -460,7 +294,6 @@ describe('Settings Loading and Merging', () => {
       expect(settings.merged).toEqual({
         ui: {
           theme: 'system-theme',
-          customThemes: {},
         },
         tools: {
           sandbox: false,
@@ -469,26 +302,10 @@ describe('Settings Loading and Merging', () => {
         telemetry: { enabled: false },
         context: {
           fileName: 'WORKSPACE_CONTEXT.md',
-          includeDirectories: [],
         },
         mcp: {
           allowed: ['server1', 'server2'],
         },
-        advanced: {
-          excludedEnvVars: [],
-        },
-        extensions: {
-          disabled: [],
-          workspacesWithMigrationNudge: [],
-        },
-        mcpServers: {},
-        model: {
-          chatCompression: {},
-        },
-        security: {},
-        general: {},
-        privacy: {},
-        ide: {},
       });
     });
 
@@ -530,18 +347,15 @@ describe('Settings Loading and Merging', () => {
       expect(settings.merged).toEqual({
         ui: {
           theme: 'legacy-dark',
-          customThemes: {},
         },
         general: {
           vimMode: true,
         },
         context: {
           fileName: 'LEGACY_CONTEXT.md',
-          includeDirectories: [],
         },
         model: {
           name: 'gemini-pro',
-          chatCompression: {},
         },
         mcpServers: {
           'legacy-server-1': {
@@ -559,21 +373,30 @@ describe('Settings Loading and Merging', () => {
           allowed: ['legacy-server-1'],
         },
         someUnrecognizedSetting: 'should-be-preserved',
-        advanced: {
-          excludedEnvVars: [],
-        },
-        extensions: {
-          disabled: [],
-          workspacesWithMigrationNudge: [],
-        },
-        security: {},
-        privacy: {},
-        telemetry: {},
-        tools: {},
-        ide: {},
       });
     });
 
+    it('should rewrite allowedTools to tools.allowed during migration', () => {
+      (mockFsExistsSync as Mock).mockImplementation(
+        (p: fs.PathLike) => p === USER_SETTINGS_PATH,
+      );
+      const legacySettingsContent = {
+        allowedTools: ['fs', 'shell'],
+      };
+      (fs.readFileSync as Mock).mockImplementation(
+        (p: fs.PathOrFileDescriptor) => {
+          if (p === USER_SETTINGS_PATH)
+            return JSON.stringify(legacySettingsContent);
+          return '{}';
+        },
+      );
+
+      const settings = loadSettings(MOCK_WORKSPACE_DIR);
+
+      expect(settings.merged.tools?.allowed).toEqual(['fs', 'shell']);
+      expect((settings.merged as TestSettings)['allowedTools']).toBeUndefined();
+    });
+
     it('should correctly merge and migrate legacy array properties from multiple scopes', () => {
       (mockFsExistsSync as Mock).mockReturnValue(true);
       const legacyUserSettings = {
@@ -678,9 +501,6 @@ describe('Settings Loading and Merging', () => {
       expect(settings.user.settings).toEqual(userSettingsContent);
       expect(settings.workspace.settings).toEqual(workspaceSettingsContent);
       expect(settings.merged).toEqual({
-        advanced: {
-          excludedEnvVars: [],
-        },
         context: {
           fileName: 'WORKSPACE_CONTEXT.md',
           includeDirectories: [
@@ -691,31 +511,17 @@ describe('Settings Loading and Merging', () => {
             '/system/dir',
           ],
         },
-        extensions: {
-          disabled: [],
-          workspacesWithMigrationNudge: [],
-        },
-        mcp: {},
-        mcpServers: {},
-        model: {
-          chatCompression: {},
-        },
-        security: {},
-        telemetry: {},
+        telemetry: false,
         tools: {
           sandbox: false,
         },
         ui: {
-          customThemes: {},
           theme: 'system-theme',
         },
-        general: {},
-        privacy: {},
-        ide: {},
       });
     });
 
-    it('should ignore folderTrust from workspace settings', () => {
+    it('should use folderTrust from workspace settings when trusted', () => {
       (mockFsExistsSync as Mock).mockReturnValue(true);
       const userSettingsContent = {
         security: {
@@ -727,7 +533,7 @@ describe('Settings Loading and Merging', () => {
       const workspaceSettingsContent = {
         security: {
           folderTrust: {
-            enabled: false, // This should be ignored
+            enabled: false, // This should be used
           },
         },
       };
@@ -748,7 +554,7 @@ describe('Settings Loading and Merging', () => {
       );
 
       const settings = loadSettings(MOCK_WORKSPACE_DIR);
-      expect(settings.merged.security?.folderTrust?.enabled).toBe(true); // User setting should be used
+      expect(settings.merged.security?.folderTrust?.enabled).toBe(false); // Workspace setting should be used
     });
 
     it('should use system folderTrust over user setting', () => {
@@ -875,7 +681,10 @@ describe('Settings Loading and Merging', () => {
     });
 
     it('should merge excludedProjectEnvVars with workspace taking precedence over user', () => {
-      (mockFsExistsSync as Mock).mockReturnValue(true);
+      (mockFsExistsSync as Mock).mockImplementation(
+        (p: fs.PathLike) =>
+          p === USER_SETTINGS_PATH || p === MOCK_WORKSPACE_SETTINGS_PATH,
+      );
       const userSettingsContent = {
         general: {},
         advanced: { excludedEnvVars: ['DEBUG', 'NODE_ENV', 'USER_VAR'] },
@@ -916,7 +725,10 @@ describe('Settings Loading and Merging', () => {
     });
 
     it('should default contextFileName to undefined if not in any settings file', () => {
-      (mockFsExistsSync as Mock).mockReturnValue(true);
+      (mockFsExistsSync as Mock).mockImplementation(
+        (p: fs.PathLike) =>
+          p === USER_SETTINGS_PATH || p === MOCK_WORKSPACE_SETTINGS_PATH,
+      );
       const userSettingsContent = { ui: { theme: 'dark' } };
       const workspaceSettingsContent = { tools: { sandbox: true } };
       (fs.readFileSync as Mock).mockImplementation(
@@ -986,13 +798,16 @@ describe('Settings Loading and Merging', () => {
       (mockFsExistsSync as Mock).mockReturnValue(false); // No settings files exist
       (fs.readFileSync as Mock).mockReturnValue('{}');
       const settings = loadSettings(MOCK_WORKSPACE_DIR);
-      expect(settings.merged.telemetry).toEqual({});
-      expect(settings.merged.ui?.customThemes).toEqual({});
-      expect(settings.merged.mcpServers).toEqual({});
+      expect(settings.merged.telemetry).toBeUndefined();
+      expect(settings.merged.ui).toBeUndefined();
+      expect(settings.merged.mcpServers).toBeUndefined();
     });
 
     it('should merge MCP servers correctly, with workspace taking precedence', () => {
-      (mockFsExistsSync as Mock).mockReturnValue(true);
+      (mockFsExistsSync as Mock).mockImplementation(
+        (p: fs.PathLike) =>
+          p === USER_SETTINGS_PATH || p === MOCK_WORKSPACE_SETTINGS_PATH,
+      );
       const userSettingsContent = {
         mcpServers: {
           'user-server': {
@@ -1110,11 +925,11 @@ describe('Settings Loading and Merging', () => {
       });
     });
 
-    it('should have mcpServers as empty object if not in any settings file', () => {
+    it('should have mcpServers as undefined if not in any settings file', () => {
       (mockFsExistsSync as Mock).mockReturnValue(false); // No settings files exist
       (fs.readFileSync as Mock).mockReturnValue('{}');
       const settings = loadSettings(MOCK_WORKSPACE_DIR);
-      expect(settings.merged.mcpServers).toEqual({});
+      expect(settings.merged.mcpServers).toBeUndefined();
     });
 
     it('should merge MCP servers from system, user, and workspace with system taking precedence', () => {
@@ -1282,11 +1097,11 @@ describe('Settings Loading and Merging', () => {
       });
     });
 
-    it('should have chatCompression as an empty object if not in any settings file', () => {
+    it('should have model as undefined if not in any settings file', () => {
       (mockFsExistsSync as Mock).mockReturnValue(false); // No settings files exist
       (fs.readFileSync as Mock).mockReturnValue('{}');
       const settings = loadSettings(MOCK_WORKSPACE_DIR);
-      expect(settings.merged.model?.chatCompression).toEqual({});
+      expect(settings.merged.model).toBeUndefined();
     });
 
     it('should ignore chatCompression if contextPercentageThreshold is invalid', () => {
@@ -1411,54 +1226,22 @@ describe('Settings Loading and Merging', () => {
         },
       );
 
-      const settings = loadSettings(MOCK_WORKSPACE_DIR);
-
-      // Check that settings are empty due to parsing errors
-      expect(settings.user.settings).toEqual({});
-      expect(settings.workspace.settings).toEqual({});
-      expect(settings.merged).toEqual({
-        ui: {
-          customThemes: {},
-        },
-        mcp: {},
-        mcpServers: {},
-        context: {
-          includeDirectories: [],
-        },
-        model: {
-          chatCompression: {},
-        },
-        advanced: {
-          excludedEnvVars: [],
-        },
-        extensions: {
-          disabled: [],
-          workspacesWithMigrationNudge: [],
-        },
-        security: {},
-        general: {},
-        privacy: {},
-        tools: {},
-        telemetry: {},
-        ide: {},
-      });
-
-      // Check that error objects are populated in settings.errors
-      expect(settings.errors).toBeDefined();
-      // Assuming both user and workspace files cause errors and are added in order
-      expect(settings.errors.length).toEqual(2);
-
-      const userError = settings.errors.find(
-        (e) => e.path === USER_SETTINGS_PATH,
-      );
-      expect(userError).toBeDefined();
-      expect(userError?.message).toBe(userReadError.message);
-
-      const workspaceError = settings.errors.find(
-        (e) => e.path === MOCK_WORKSPACE_SETTINGS_PATH,
-      );
-      expect(workspaceError).toBeDefined();
-      expect(workspaceError?.message).toBe(workspaceReadError.message);
+      try {
+        loadSettings(MOCK_WORKSPACE_DIR);
+        fail('loadSettings should have thrown a FatalConfigError');
+      } catch (e) {
+        expect(e).toBeInstanceOf(FatalConfigError);
+        const error = e as FatalConfigError;
+        expect(error.message).toContain(
+          `Error in ${USER_SETTINGS_PATH}: ${userReadError.message}`,
+        );
+        expect(error.message).toContain(
+          `Error in ${MOCK_WORKSPACE_SETTINGS_PATH}: ${workspaceReadError.message}`,
+        );
+        expect(error.message).toContain(
+          'Please fix the configuration file(s) and try again.',
+        );
+      }
 
       // Restore JSON.parse mock if it was spied on specifically for this test
       vi.restoreAllMocks(); // Or more targeted restore if needed
@@ -1849,30 +1632,6 @@ describe('Settings Loading and Merging', () => {
         expect(settings.system.settings).toEqual(systemSettingsContent);
         expect(settings.merged).toEqual({
           ...systemSettingsContent,
-          ui: {
-            ...systemSettingsContent.ui,
-            customThemes: {},
-          },
-          mcp: {},
-          mcpServers: {},
-          context: {
-            includeDirectories: [],
-          },
-          model: {
-            chatCompression: {},
-          },
-          advanced: {
-            excludedEnvVars: [],
-          },
-          extensions: {
-            disabled: [],
-            workspacesWithMigrationNudge: [],
-          },
-          security: {},
-          general: {},
-          privacy: {},
-          telemetry: {},
-          ide: {},
         });
       });
     });
@@ -2408,4 +2167,121 @@ describe('Settings Loading and Merging', () => {
       });
     });
   });
+
+  describe('loadEnvironment', () => {
+    function setup({
+      isFolderTrustEnabled = true,
+      isWorkspaceTrustedValue = true,
+    }) {
+      delete process.env['TESTTEST']; // reset
+      const geminiEnvPath = path.resolve(path.join(GEMINI_DIR, '.env'));
+
+      vi.mocked(isWorkspaceTrusted).mockReturnValue(isWorkspaceTrustedValue);
+      (mockFsExistsSync as Mock).mockImplementation((p: fs.PathLike) =>
+        [USER_SETTINGS_PATH, geminiEnvPath].includes(p.toString()),
+      );
+      const userSettingsContent: Settings = {
+        ui: {
+          theme: 'dark',
+        },
+        security: {
+          folderTrust: {
+            enabled: isFolderTrustEnabled,
+          },
+        },
+        context: {
+          fileName: 'USER_CONTEXT.md',
+        },
+      };
+      (fs.readFileSync as Mock).mockImplementation(
+        (p: fs.PathOrFileDescriptor) => {
+          if (p === USER_SETTINGS_PATH)
+            return JSON.stringify(userSettingsContent);
+          if (p === geminiEnvPath) return 'TESTTEST=1234';
+          return '{}';
+        },
+      );
+    }
+
+    it('sets environment variables from .env files', () => {
+      setup({ isFolderTrustEnabled: false, isWorkspaceTrustedValue: true });
+      loadEnvironment(loadSettings(MOCK_WORKSPACE_DIR).merged);
+
+      expect(process.env['TESTTEST']).toEqual('1234');
+    });
+
+    it('does not load env files from untrusted spaces', () => {
+      setup({ isFolderTrustEnabled: true, isWorkspaceTrustedValue: false });
+      loadEnvironment(loadSettings(MOCK_WORKSPACE_DIR).merged);
+
+      expect(process.env['TESTTEST']).not.toEqual('1234');
+    });
+  });
+
+  describe('needsMigration', () => {
+    it('should return false for an empty object', () => {
+      expect(needsMigration({})).toBe(false);
+    });
+
+    it('should return false for settings that are already in V2 format', () => {
+      const v2Settings = {
+        ui: {
+          theme: 'dark',
+        },
+        tools: {
+          sandbox: true,
+        },
+      };
+      expect(needsMigration(v2Settings)).toBe(false);
+    });
+
+    it('should return true for settings with a V1 key that needs to be moved', () => {
+      const v1Settings = {
+        theme: 'dark', // v1 key
+      };
+      expect(needsMigration(v1Settings)).toBe(true);
+    });
+
+    it('should return true for settings with a mix of V1 and V2 keys', () => {
+      const mixedSettings = {
+        theme: 'dark', // v1 key
+        tools: {
+          sandbox: true, // v2 key
+        },
+      };
+      expect(needsMigration(mixedSettings)).toBe(true);
+    });
+
+    it('should return false for settings with only V1 keys that are the same in V2', () => {
+      const v1Settings = {
+        mcpServers: {},
+        telemetry: {},
+        extensions: [],
+      };
+      expect(needsMigration(v1Settings)).toBe(false);
+    });
+
+    it('should return true for settings with a mix of V1 keys that are the same in V2 and V1 keys that need moving', () => {
+      const v1Settings = {
+        mcpServers: {}, // same in v2
+        theme: 'dark', // needs moving
+      };
+      expect(needsMigration(v1Settings)).toBe(true);
+    });
+
+    it('should return false for settings with unrecognized keys', () => {
+      const settings = {
+        someUnrecognizedKey: 'value',
+      };
+      expect(needsMigration(settings)).toBe(false);
+    });
+
+    it('should return false for settings with v2 keys and unrecognized keys', () => {
+      const settings = {
+        ui: { theme: 'dark' },
+        someUnrecognizedKey: 'value',
+      };
+      expect(needsMigration(settings)).toBe(false);
+    });
+  });
 });

packages/cli/src/config/settings.ts

@@ -8,7 +8,9 @@ import * as fs from 'node:fs';
 import * as path from 'node:path';
 import { homedir, platform } from 'node:os';
 import * as dotenv from 'dotenv';
+import process from 'node:process';
 import {
+  FatalConfigError,
   GEMINI_CONFIG_DIR as GEMINI_DIR,
   getErrorMessage,
   Storage,
@@ -17,8 +19,31 @@ import stripJsonComments from 'strip-json-comments';
 import { DefaultLight } from '../ui/themes/default-light.js';
 import { DefaultDark } from '../ui/themes/default.js';
 import { isWorkspaceTrusted } from './trustedFolders.js';
-import type { Settings, MemoryImportFormat } from './settingsSchema.js';
-import { mergeWith } from 'lodash-es';
+import {
+  type Settings,
+  type MemoryImportFormat,
+  type MergeStrategy,
+  type SettingsSchema,
+  type SettingDefinition,
+  getSettingsSchema,
+} from './settingsSchema.js';
+import { resolveEnvVarsInObject } from '../utils/envVarResolver.js';
+import { customDeepMerge } from '../utils/deepMerge.js';
+
+function getMergeStrategyForPath(path: string[]): MergeStrategy | undefined {
+  let current: SettingDefinition | undefined = undefined;
+  let currentSchema: SettingsSchema | undefined = getSettingsSchema();
+
+  for (const key of path) {
+    if (!currentSchema || !currentSchema[key]) {
+      return undefined;
+    }
+    current = currentSchema[key];
+    currentSchema = current.properties;
+  }
+
+  return current?.mergeStrategy;
+}
 
 export type { Settings, MemoryImportFormat };
 
@@ -31,53 +56,66 @@ export const DEFAULT_EXCLUDED_ENV_VARS = ['DEBUG', 'DEBUG_MODE'];
 const MIGRATE_V2_OVERWRITE = false;
 
 const MIGRATION_MAP: Record<string, string> = {
-  preferredEditor: 'general.preferredEditor',
-  vimMode: 'general.vimMode',
+  accessibility: 'ui.accessibility',
+  allowedTools: 'tools.allowed',
+  allowMCPServers: 'mcp.allowed',
+  autoAccept: 'tools.autoAccept',
+  autoConfigureMaxOldSpaceSize: 'advanced.autoConfigureMemory',
+  bugCommand: 'advanced.bugCommand',
+  chatCompression: 'model.chatCompression',
+  checkpointing: 'general.checkpointing',
+  coreTools: 'tools.core',
+  contextFileName: 'context.fileName',
+  customThemes: 'ui.customThemes',
+  debugKeystrokeLogging: 'general.debugKeystrokeLogging',
   disableAutoUpdate: 'general.disableAutoUpdate',
   disableUpdateNag: 'general.disableUpdateNag',
-  checkpointing: 'general.checkpointing',
-  theme: 'ui.theme',
-  customThemes: 'ui.customThemes',
+  dnsResolutionOrder: 'advanced.dnsResolutionOrder',
+  enablePromptCompletion: 'general.enablePromptCompletion',
+  enforcedAuthType: 'security.auth.enforcedType',
+  excludeTools: 'tools.exclude',
+  excludeMCPServers: 'mcp.excluded',
+  excludedProjectEnvVars: 'advanced.excludedEnvVars',
+  extensionManagement: 'experimental.extensionManagement',
+  extensions: 'extensions',
+  fileFiltering: 'context.fileFiltering',
+  folderTrustFeature: 'security.folderTrust.featureEnabled',
+  folderTrust: 'security.folderTrust.enabled',
+  hasSeenIdeIntegrationNudge: 'ide.hasSeenNudge',
   hideWindowTitle: 'ui.hideWindowTitle',
   hideTips: 'ui.hideTips',
   hideBanner: 'ui.hideBanner',
   hideFooter: 'ui.hideFooter',
+  hideCWD: 'ui.footer.hideCWD',
+  hideSandboxStatus: 'ui.footer.hideSandboxStatus',
+  hideModelInfo: 'ui.footer.hideModelInfo',
+  hideContextSummary: 'ui.hideContextSummary',
   showMemoryUsage: 'ui.showMemoryUsage',
   showLineNumbers: 'ui.showLineNumbers',
-  accessibility: 'ui.accessibility',
+  showCitations: 'ui.showCitations',
   ideMode: 'ide.enabled',
-  hasSeenIdeIntegrationNudge: 'ide.hasSeenNudge',
-  usageStatisticsEnabled: 'privacy.usageStatisticsEnabled',
-  telemetry: 'telemetry',
-  model: 'model.name',
-  maxSessionTurns: 'model.maxSessionTurns',
-  summarizeToolOutput: 'model.summarizeToolOutput',
-  chatCompression: 'model.chatCompression',
-  skipNextSpeakerCheck: 'model.skipNextSpeakerCheck',
-  contextFileName: 'context.fileName',
-  memoryImportFormat: 'context.importFormat',
-  memoryDiscoveryMaxDirs: 'context.discoveryMaxDirs',
   includeDirectories: 'context.includeDirectories',
   loadMemoryFromIncludeDirectories: 'context.loadFromIncludeDirectories',
-  fileFiltering: 'context.fileFiltering',
+  maxSessionTurns: 'model.maxSessionTurns',
+  mcpServers: 'mcpServers',
+  mcpServerCommand: 'mcp.serverCommand',
+  memoryImportFormat: 'context.importFormat',
+  memoryDiscoveryMaxDirs: 'context.discoveryMaxDirs',
+  model: 'model.name',
+  preferredEditor: 'general.preferredEditor',
   sandbox: 'tools.sandbox',
+  selectedAuthType: 'security.auth.selectedType',
   shouldUseNodePtyShell: 'tools.usePty',
-  allowedTools: 'tools.allowed',
-  coreTools: 'tools.core',
-  excludeTools: 'tools.exclude',
+  skipNextSpeakerCheck: 'model.skipNextSpeakerCheck',
+  summarizeToolOutput: 'model.summarizeToolOutput',
+  telemetry: 'telemetry',
+  theme: 'ui.theme',
   toolDiscoveryCommand: 'tools.discoveryCommand',
   toolCallCommand: 'tools.callCommand',
-  mcpServerCommand: 'mcp.serverCommand',
-  allowMCPServers: 'mcp.allowed',
-  excludeMCPServers: 'mcp.excluded',
-  folderTrustFeature: 'security.folderTrust.featureEnabled',
-  folderTrust: 'security.folderTrust.enabled',
-  selectedAuthType: 'security.auth.selectedType',
+  usageStatisticsEnabled: 'privacy.usageStatisticsEnabled',
   useExternalAuth: 'security.auth.useExternal',
-  autoConfigureMaxOldSpaceSize: 'advanced.autoConfigureMemory',
-  dnsResolutionOrder: 'advanced.dnsResolutionOrder',
-  excludedProjectEnvVars: 'advanced.excludedEnvVars',
-  bugCommand: 'advanced.bugCommand',
+  useRipgrep: 'tools.useRipgrep',
+  vimMode: 'general.vimMode',
 };
 
 export function getSystemSettingsPath(): string {
@@ -160,8 +198,27 @@ function setNestedProperty(
   current[lastKey] = value;
 }
 
-function needsMigration(settings: Record<string, unknown>): boolean {
-  return !('general' in settings);
+export function needsMigration(settings: Record<string, unknown>): boolean {
+  // A file needs migration if it contains any top-level key that is moved to a
+  // nested location in V2.
+  const hasV1Keys = Object.entries(MIGRATION_MAP).some(([v1Key, v2Path]) => {
+    if (v1Key === v2Path || !(v1Key in settings)) {
+      return false;
+    }
+    // If a key exists that is both a V1 key and a V2 container (like 'model'),
+    // we need to check the type. If it's an object, it's a V2 container and not
+    // a V1 key that needs migration.
+    if (
+      KNOWN_V2_CONTAINERS.has(v1Key) &&
+      typeof settings[v1Key] === 'object' &&
+      settings[v1Key] !== null
+    ) {
+      return false;
+    }
+    return true;
+  });
+
+  return hasV1Keys;
 }
 
 function migrateSettingsToV2(
@@ -272,155 +329,20 @@ function mergeSettings(
 ): Settings {
   const safeWorkspace = isTrusted ? workspace : ({} as Settings);
 
-  // folderTrust is not supported at workspace level.
-  const { security, ...restOfWorkspace } = safeWorkspace;
-  const safeWorkspaceWithoutFolderTrust = security
-    ? {
-        ...restOfWorkspace,
-        // eslint-disable-next-line @typescript-eslint/no-unused-vars
-        security: (({ folderTrust, ...rest }) => rest)(security),
-      }
-    : {
-        ...restOfWorkspace,
-        security: {},
-      };
-
   // Settings are merged with the following precedence (last one wins for
   // single values):
   // 1. System Defaults
   // 2. User Settings
   // 3. Workspace Settings
   // 4. System Settings (as overrides)
-  //
-  // For properties that are arrays (e.g., includeDirectories), the arrays
-  // are concatenated. For objects (e.g., customThemes), they are merged.
-  return {
-    ...systemDefaults,
-    ...user,
-    ...safeWorkspaceWithoutFolderTrust,
-    ...system,
-    general: {
-      ...(systemDefaults.general || {}),
-      ...(user.general || {}),
-      ...(safeWorkspaceWithoutFolderTrust.general || {}),
-      ...(system.general || {}),
-    },
-    ui: {
-      ...(systemDefaults.ui || {}),
-      ...(user.ui || {}),
-      ...(safeWorkspaceWithoutFolderTrust.ui || {}),
-      ...(system.ui || {}),
-      customThemes: {
-        ...(systemDefaults.ui?.customThemes || {}),
-        ...(user.ui?.customThemes || {}),
-        ...(safeWorkspaceWithoutFolderTrust.ui?.customThemes || {}),
-        ...(system.ui?.customThemes || {}),
-      },
-    },
-    ide: {
-      ...(systemDefaults.ide || {}),
-      ...(user.ide || {}),
-      ...(safeWorkspaceWithoutFolderTrust.ide || {}),
-      ...(system.ide || {}),
-    },
-    privacy: {
-      ...(systemDefaults.privacy || {}),
-      ...(user.privacy || {}),
-      ...(safeWorkspaceWithoutFolderTrust.privacy || {}),
-      ...(system.privacy || {}),
-    },
-    telemetry: {
-      ...(systemDefaults.telemetry || {}),
-      ...(user.telemetry || {}),
-      ...(safeWorkspaceWithoutFolderTrust.telemetry || {}),
-      ...(system.telemetry || {}),
-    },
-    security: {
-      ...(systemDefaults.security || {}),
-      ...(user.security || {}),
-      ...(safeWorkspaceWithoutFolderTrust.security || {}),
-      ...(system.security || {}),
-    },
-    mcp: {
-      ...(systemDefaults.mcp || {}),
-      ...(user.mcp || {}),
-      ...(safeWorkspaceWithoutFolderTrust.mcp || {}),
-      ...(system.mcp || {}),
-    },
-    mcpServers: {
-      ...(systemDefaults.mcpServers || {}),
-      ...(user.mcpServers || {}),
-      ...(safeWorkspaceWithoutFolderTrust.mcpServers || {}),
-      ...(system.mcpServers || {}),
-    },
-    tools: {
-      ...(systemDefaults.tools || {}),
-      ...(user.tools || {}),
-      ...(safeWorkspaceWithoutFolderTrust.tools || {}),
-      ...(system.tools || {}),
-    },
-    context: {
-      ...(systemDefaults.context || {}),
-      ...(user.context || {}),
-      ...(safeWorkspaceWithoutFolderTrust.context || {}),
-      ...(system.context || {}),
-      includeDirectories: [
-        ...(systemDefaults.context?.includeDirectories || []),
-        ...(user.context?.includeDirectories || []),
-        ...(safeWorkspaceWithoutFolderTrust.context?.includeDirectories || []),
-        ...(system.context?.includeDirectories || []),
-      ],
-    },
-    model: {
-      ...(systemDefaults.model || {}),
-      ...(user.model || {}),
-      ...(safeWorkspaceWithoutFolderTrust.model || {}),
-      ...(system.model || {}),
-      chatCompression: {
-        ...(systemDefaults.model?.chatCompression || {}),
-        ...(user.model?.chatCompression || {}),
-        ...(safeWorkspaceWithoutFolderTrust.model?.chatCompression || {}),
-        ...(system.model?.chatCompression || {}),
-      },
-    },
-    advanced: {
-      ...(systemDefaults.advanced || {}),
-      ...(user.advanced || {}),
-      ...(safeWorkspaceWithoutFolderTrust.advanced || {}),
-      ...(system.advanced || {}),
-      excludedEnvVars: [
-        ...new Set([
-          ...(systemDefaults.advanced?.excludedEnvVars || []),
-          ...(user.advanced?.excludedEnvVars || []),
-          ...(safeWorkspaceWithoutFolderTrust.advanced?.excludedEnvVars || []),
-          ...(system.advanced?.excludedEnvVars || []),
-        ]),
-      ],
-    },
-    extensions: {
-      ...(systemDefaults.extensions || {}),
-      ...(user.extensions || {}),
-      ...(safeWorkspaceWithoutFolderTrust.extensions || {}),
-      ...(system.extensions || {}),
-      disabled: [
-        ...new Set([
-          ...(systemDefaults.extensions?.disabled || []),
-          ...(user.extensions?.disabled || []),
-          ...(safeWorkspaceWithoutFolderTrust.extensions?.disabled || []),
-          ...(system.extensions?.disabled || []),
-        ]),
-      ],
-      workspacesWithMigrationNudge: [
-        ...new Set([
-          ...(systemDefaults.extensions?.workspacesWithMigrationNudge || []),
-          ...(user.extensions?.workspacesWithMigrationNudge || []),
-          ...(safeWorkspaceWithoutFolderTrust.extensions
-            ?.workspacesWithMigrationNudge || []),
-          ...(system.extensions?.workspacesWithMigrationNudge || []),
-        ]),
-      ],
-    },
-  };
+  return customDeepMerge(
+    getMergeStrategyForPath,
+    {}, // Start with an empty object
+    systemDefaults,
+    user,
+    safeWorkspace,
+    system,
+  ) as Settings;
 }
 
 export class LoadedSettings {
@@ -429,7 +351,6 @@ export class LoadedSettings {
     systemDefaults: SettingsFile,
     user: SettingsFile,
     workspace: SettingsFile,
-    errors: SettingsError[],
     isTrusted: boolean,
     migratedInMemorScopes: Set<SettingScope>,
   ) {
@@ -437,7 +358,6 @@ export class LoadedSettings {
     this.systemDefaults = systemDefaults;
     this.user = user;
     this.workspace = workspace;
-    this.errors = errors;
     this.isTrusted = isTrusted;
     this.migratedInMemorScopes = migratedInMemorScopes;
     this._merged = this.computeMergedSettings();
@@ -447,7 +367,6 @@ export class LoadedSettings {
   readonly systemDefaults: SettingsFile;
   readonly user: SettingsFile;
   readonly workspace: SettingsFile;
-  readonly errors: SettingsError[];
   readonly isTrusted: boolean;
   readonly migratedInMemorScopes: Set<SettingScope>;
 
@@ -490,48 +409,6 @@ export class LoadedSettings {
   }
 }
 
-function resolveEnvVarsInString(value: string): string {
-  const envVarRegex = /\$(?:(\w+)|{([^}]+)})/g; // Find $VAR_NAME or ${VAR_NAME}
-  return value.replace(envVarRegex, (match, varName1, varName2) => {
-    const varName = varName1 || varName2;
-    if (process && process.env && typeof process.env[varName] === 'string') {
-      return process.env[varName]!;
-    }
-    return match;
-  });
-}
-
-function resolveEnvVarsInObject<T>(obj: T): T {
-  if (
-    obj === null ||
-    obj === undefined ||
-    typeof obj === 'boolean' ||
-    typeof obj === 'number'
-  ) {
-    return obj;
-  }
-
-  if (typeof obj === 'string') {
-    return resolveEnvVarsInString(obj) as unknown as T;
-  }
-
-  if (Array.isArray(obj)) {
-    return obj.map((item) => resolveEnvVarsInObject(item)) as unknown as T;
-  }
-
-  if (typeof obj === 'object') {
-    const newObj = { ...obj } as T;
-    for (const key in newObj) {
-      if (Object.prototype.hasOwnProperty.call(newObj, key)) {
-        newObj[key] = resolveEnvVarsInObject(newObj[key]);
-      }
-    }
-    return newObj;
-  }
-
-  return obj;
-}
-
 function findEnvFile(startDir: string): string | null {
   let currentDir = path.resolve(startDir);
   while (true) {
@@ -583,36 +460,18 @@ export function setUpCloudShellEnvironment(envFilePath: string | null): void {
   }
 }
 
-export function loadEnvironment(settings?: Settings): void {
+export function loadEnvironment(settings: Settings): void {
   const envFilePath = findEnvFile(process.cwd());
 
+  if (!isWorkspaceTrusted(settings)) {
+    return;
+  }
+
   // Cloud Shell environment variable handling
   if (process.env['CLOUD_SHELL'] === 'true') {
     setUpCloudShellEnvironment(envFilePath);
   }
 
-  // If no settings provided, try to load workspace settings for exclusions
-  let resolvedSettings = settings;
-  if (!resolvedSettings) {
-    const workspaceSettingsPath = new Storage(
-      process.cwd(),
-    ).getWorkspaceSettingsPath();
-    try {
-      if (fs.existsSync(workspaceSettingsPath)) {
-        const workspaceContent = fs.readFileSync(
-          workspaceSettingsPath,
-          'utf-8',
-        );
-        const parsedWorkspaceSettings = JSON.parse(
-          stripJsonComments(workspaceContent),
-        ) as Settings;
-        resolvedSettings = resolveEnvVarsInObject(parsedWorkspaceSettings);
-      }
-    } catch (_e) {
-      // Ignore errors loading workspace settings
-    }
-  }
-
   if (envFilePath) {
     // Manually parse and load environment variables to handle exclusions correctly.
     // This avoids modifying environment variables that were already set from the shell.
@@ -621,8 +480,7 @@ export function loadEnvironment(settings?: Settings): void {
       const parsedEnv = dotenv.parse(envFileContent);
 
       const excludedVars =
-        resolvedSettings?.advanced?.excludedEnvVars ||
-        DEFAULT_EXCLUDED_ENV_VARS;
+        settings?.advanced?.excludedEnvVars || DEFAULT_EXCLUDED_ENV_VARS;
       const isProjectEnvFile = !envFilePath.includes(GEMINI_DIR);
 
       for (const key in parsedEnv) {
@@ -648,7 +506,9 @@ export function loadEnvironment(settings?: Settings): void {
  * Loads settings from user and workspace directories.
  * Project settings override user settings.
  */
-export function loadSettings(workspaceDir: string): LoadedSettings {
+export function loadSettings(
+  workspaceDir: string = process.cwd(),
+): LoadedSettings {
   let systemSettings: Settings = {};
   let systemDefaultSettings: Settings = {};
   let userSettings: Settings = {};
@@ -758,7 +618,12 @@ export function loadSettings(workspaceDir: string): LoadedSettings {
   }
 
   // For the initial trust check, we can only use user and system settings.
-  const initialTrustCheckSettings = mergeWith({}, systemSettings, userSettings);
+  const initialTrustCheckSettings = customDeepMerge(
+    getMergeStrategyForPath,
+    {},
+    systemSettings,
+    userSettings,
+  );
   const isTrusted =
     isWorkspaceTrusted(initialTrustCheckSettings as Settings) ?? true;
 
@@ -781,7 +646,17 @@ export function loadSettings(workspaceDir: string): LoadedSettings {
   workspaceSettings = resolveEnvVarsInObject(workspaceSettings);
 
   // Create LoadedSettings first
-  const loadedSettings = new LoadedSettings(
+
+  if (settingsErrors.length > 0) {
+    const errorMessages = settingsErrors.map(
+      (error) => `Error in ${error.path}: ${error.message}`,
+    );
+    throw new FatalConfigError(
+      `${errorMessages.join('\n')}\nPlease fix the configuration file(s) and try again.`,
+    );
+  }
+
+  return new LoadedSettings(
     {
       path: systemSettingsPath,
       settings: systemSettings,
@@ -798,12 +673,9 @@ export function loadSettings(workspaceDir: string): LoadedSettings {
       path: workspaceSettingsPath,
       settings: workspaceSettings,
     },
-    settingsErrors,
     isTrusted,
     migratedInMemorScopes,
   );
-
-  return loadedSettings;
 }
 
 export function saveSettings(settingsFile: SettingsFile): void {

packages/cli/src/config/settingsSchema.test.ts

@@ -5,13 +5,17 @@
  */
 
 import { describe, it, expect } from 'vitest';
-import type { Settings } from './settingsSchema.js';
-import { SETTINGS_SCHEMA } from './settingsSchema.js';
+import {
+  getSettingsSchema,
+  type SettingDefinition,
+  type Settings,
+  type SettingsSchema,
+} from './settingsSchema.js';
 
 describe('SettingsSchema', () => {
-  describe('SETTINGS_SCHEMA', () => {
+  describe('getSettingsSchema', () => {
     it('should contain all expected top-level settings', () => {
-      const expectedSettings = [
+      const expectedSettings: Array<keyof Settings> = [
         'mcpServers',
         'general',
         'ui',
@@ -27,14 +31,12 @@ describe('SettingsSchema', () => {
       ];
 
       expectedSettings.forEach((setting) => {
-        expect(
-          SETTINGS_SCHEMA[setting as keyof typeof SETTINGS_SCHEMA],
-        ).toBeDefined();
+        expect(getSettingsSchema()[setting as keyof Settings]).toBeDefined();
       });
     });
 
     it('should have correct structure for each setting', () => {
-      Object.entries(SETTINGS_SCHEMA).forEach(([_key, definition]) => {
+      Object.entries(getSettingsSchema()).forEach(([_key, definition]) => {
         expect(definition).toHaveProperty('type');
         expect(definition).toHaveProperty('label');
         expect(definition).toHaveProperty('category');
@@ -48,7 +50,7 @@ describe('SettingsSchema', () => {
     });
 
     it('should have correct nested setting structure', () => {
-      const nestedSettings = [
+      const nestedSettings: Array<keyof Settings> = [
         'general',
         'ui',
         'ide',
@@ -62,11 +64,9 @@ describe('SettingsSchema', () => {
       ];
 
       nestedSettings.forEach((setting) => {
-        const definition = SETTINGS_SCHEMA[
-          setting as keyof typeof SETTINGS_SCHEMA
-        ] as (typeof SETTINGS_SCHEMA)[keyof typeof SETTINGS_SCHEMA] & {
-          properties: unknown;
-        };
+        const definition = getSettingsSchema()[
+          setting as keyof Settings
+        ] as SettingDefinition;
         expect(definition.type).toBe('object');
         expect(definition.properties).toBeDefined();
         expect(typeof definition.properties).toBe('object');
@@ -75,35 +75,36 @@ describe('SettingsSchema', () => {
 
     it('should have accessibility nested properties', () => {
       expect(
-        SETTINGS_SCHEMA.ui?.properties?.accessibility?.properties,
+        getSettingsSchema().ui?.properties?.accessibility?.properties,
       ).toBeDefined();
       expect(
-        SETTINGS_SCHEMA.ui?.properties?.accessibility.properties
+        getSettingsSchema().ui?.properties?.accessibility.properties
           ?.disableLoadingPhrases.type,
       ).toBe('boolean');
     });
 
     it('should have checkpointing nested properties', () => {
       expect(
-        SETTINGS_SCHEMA.general?.properties?.checkpointing.properties?.enabled,
+        getSettingsSchema().general?.properties?.checkpointing.properties
+          ?.enabled,
       ).toBeDefined();
       expect(
-        SETTINGS_SCHEMA.general?.properties?.checkpointing.properties?.enabled
-          .type,
+        getSettingsSchema().general?.properties?.checkpointing.properties
+          ?.enabled.type,
       ).toBe('boolean');
     });
 
     it('should have fileFiltering nested properties', () => {
       expect(
-        SETTINGS_SCHEMA.context.properties.fileFiltering.properties
+        getSettingsSchema().context.properties.fileFiltering.properties
           ?.respectGitIgnore,
       ).toBeDefined();
       expect(
-        SETTINGS_SCHEMA.context.properties.fileFiltering.properties
+        getSettingsSchema().context.properties.fileFiltering.properties
           ?.respectGeminiIgnore,
       ).toBeDefined();
       expect(
-        SETTINGS_SCHEMA.context.properties.fileFiltering.properties
+        getSettingsSchema().context.properties.fileFiltering.properties
           ?.enableRecursiveFileSearch,
       ).toBeDefined();
     });
@@ -112,7 +113,7 @@ describe('SettingsSchema', () => {
       const categories = new Set();
 
       // Collect categories from top-level settings
-      Object.values(SETTINGS_SCHEMA).forEach((definition) => {
+      Object.values(getSettingsSchema()).forEach((definition) => {
         categories.add(definition.category);
         // Also collect from nested properties
         const defWithProps = definition as typeof definition & {
@@ -137,74 +138,80 @@ describe('SettingsSchema', () => {
     });
 
     it('should have consistent default values for boolean settings', () => {
-      const checkBooleanDefaults = (schema: Record<string, unknown>) => {
-        Object.entries(schema).forEach(
-          ([_key, definition]: [string, unknown]) => {
-            const def = definition as {
-              type?: string;
-              default?: unknown;
-              properties?: Record<string, unknown>;
-            };
-            if (def.type === 'boolean') {
-              // Boolean settings can have boolean or undefined defaults (for optional settings)
-              expect(['boolean', 'undefined']).toContain(typeof def.default);
-            }
-            if (def.properties) {
-              checkBooleanDefaults(def.properties);
-            }
-          },
-        );
+      const checkBooleanDefaults = (schema: SettingsSchema) => {
+        Object.entries(schema).forEach(([, definition]) => {
+          const def = definition as SettingDefinition;
+          if (def.type === 'boolean') {
+            // Boolean settings can have boolean or undefined defaults (for optional settings)
+            expect(['boolean', 'undefined']).toContain(typeof def.default);
+          }
+          if (def.properties) {
+            checkBooleanDefaults(def.properties);
+          }
+        });
       };
 
-      checkBooleanDefaults(SETTINGS_SCHEMA as Record<string, unknown>);
+      checkBooleanDefaults(getSettingsSchema() as SettingsSchema);
     });
 
     it('should have showInDialog property configured', () => {
       // Check that user-facing settings are marked for dialog display
-      expect(SETTINGS_SCHEMA.ui.properties.showMemoryUsage.showInDialog).toBe(
-        true,
-      );
-      expect(SETTINGS_SCHEMA.general.properties.vimMode.showInDialog).toBe(
-        true,
-      );
-      expect(SETTINGS_SCHEMA.ide.properties.enabled.showInDialog).toBe(true);
       expect(
-        SETTINGS_SCHEMA.general.properties.disableAutoUpdate.showInDialog,
+        getSettingsSchema().ui.properties.showMemoryUsage.showInDialog,
       ).toBe(true);
-      expect(SETTINGS_SCHEMA.ui.properties.hideWindowTitle.showInDialog).toBe(
+      expect(getSettingsSchema().general.properties.vimMode.showInDialog).toBe(
+        true,
+      );
+      expect(getSettingsSchema().ide.properties.enabled.showInDialog).toBe(
         true,
       );
-      expect(SETTINGS_SCHEMA.ui.properties.hideTips.showInDialog).toBe(true);
-      expect(SETTINGS_SCHEMA.ui.properties.hideBanner.showInDialog).toBe(true);
       expect(
-        SETTINGS_SCHEMA.privacy.properties.usageStatisticsEnabled.showInDialog,
+        getSettingsSchema().general.properties.disableAutoUpdate.showInDialog,
+      ).toBe(true);
+      expect(
+        getSettingsSchema().ui.properties.hideWindowTitle.showInDialog,
+      ).toBe(true);
+      expect(getSettingsSchema().ui.properties.hideTips.showInDialog).toBe(
+        true,
+      );
+      expect(getSettingsSchema().ui.properties.hideBanner.showInDialog).toBe(
+        true,
+      );
+      expect(
+        getSettingsSchema().privacy.properties.usageStatisticsEnabled
+          .showInDialog,
       ).toBe(false);
 
       // Check that advanced settings are hidden from dialog
-      expect(SETTINGS_SCHEMA.security.properties.auth.showInDialog).toBe(false);
-      expect(SETTINGS_SCHEMA.tools.properties.core.showInDialog).toBe(false);
-      expect(SETTINGS_SCHEMA.mcpServers.showInDialog).toBe(false);
-      expect(SETTINGS_SCHEMA.telemetry.showInDialog).toBe(false);
+      expect(getSettingsSchema().security.properties.auth.showInDialog).toBe(
+        false,
+      );
+      expect(getSettingsSchema().tools.properties.core.showInDialog).toBe(
+        false,
+      );
+      expect(getSettingsSchema().mcpServers.showInDialog).toBe(false);
+      expect(getSettingsSchema().telemetry.showInDialog).toBe(false);
 
       // Check that some settings are appropriately hidden
-      expect(SETTINGS_SCHEMA.ui.properties.theme.showInDialog).toBe(false); // Changed to false
-      expect(SETTINGS_SCHEMA.ui.properties.customThemes.showInDialog).toBe(
+      expect(getSettingsSchema().ui.properties.theme.showInDialog).toBe(false); // Changed to false
+      expect(getSettingsSchema().ui.properties.customThemes.showInDialog).toBe(
         false,
       ); // Managed via theme editor
       expect(
-        SETTINGS_SCHEMA.general.properties.checkpointing.showInDialog,
+        getSettingsSchema().general.properties.checkpointing.showInDialog,
       ).toBe(false); // Experimental feature
-      expect(SETTINGS_SCHEMA.ui.properties.accessibility.showInDialog).toBe(
+      expect(getSettingsSchema().ui.properties.accessibility.showInDialog).toBe(
         false,
       ); // Changed to false
       expect(
-        SETTINGS_SCHEMA.context.properties.fileFiltering.showInDialog,
+        getSettingsSchema().context.properties.fileFiltering.showInDialog,
       ).toBe(false); // Changed to false
       expect(
-        SETTINGS_SCHEMA.general.properties.preferredEditor.showInDialog,
+        getSettingsSchema().general.properties.preferredEditor.showInDialog,
       ).toBe(false); // Changed to false
       expect(
-        SETTINGS_SCHEMA.advanced.properties.autoConfigureMemory.showInDialog,
+        getSettingsSchema().advanced.properties.autoConfigureMemory
+          .showInDialog,
       ).toBe(false);
     });
 
@@ -228,80 +235,84 @@ describe('SettingsSchema', () => {
 
     it('should have includeDirectories setting in schema', () => {
       expect(
-        SETTINGS_SCHEMA.context?.properties.includeDirectories,
+        getSettingsSchema().context?.properties.includeDirectories,
       ).toBeDefined();
-      expect(SETTINGS_SCHEMA.context?.properties.includeDirectories.type).toBe(
-        'array',
-      );
       expect(
-        SETTINGS_SCHEMA.context?.properties.includeDirectories.category,
+        getSettingsSchema().context?.properties.includeDirectories.type,
+      ).toBe('array');
+      expect(
+        getSettingsSchema().context?.properties.includeDirectories.category,
       ).toBe('Context');
       expect(
-        SETTINGS_SCHEMA.context?.properties.includeDirectories.default,
+        getSettingsSchema().context?.properties.includeDirectories.default,
       ).toEqual([]);
     });
 
     it('should have loadMemoryFromIncludeDirectories setting in schema', () => {
       expect(
-        SETTINGS_SCHEMA.context?.properties.loadMemoryFromIncludeDirectories,
+        getSettingsSchema().context?.properties
+          .loadMemoryFromIncludeDirectories,
       ).toBeDefined();
       expect(
-        SETTINGS_SCHEMA.context?.properties.loadMemoryFromIncludeDirectories
+        getSettingsSchema().context?.properties.loadMemoryFromIncludeDirectories
           .type,
       ).toBe('boolean');
       expect(
-        SETTINGS_SCHEMA.context?.properties.loadMemoryFromIncludeDirectories
+        getSettingsSchema().context?.properties.loadMemoryFromIncludeDirectories
           .category,
       ).toBe('Context');
       expect(
-        SETTINGS_SCHEMA.context?.properties.loadMemoryFromIncludeDirectories
+        getSettingsSchema().context?.properties.loadMemoryFromIncludeDirectories
           .default,
       ).toBe(false);
     });
 
     it('should have folderTrustFeature setting in schema', () => {
       expect(
-        SETTINGS_SCHEMA.security.properties.folderTrust.properties.enabled,
+        getSettingsSchema().security.properties.folderTrust.properties.enabled,
       ).toBeDefined();
       expect(
-        SETTINGS_SCHEMA.security.properties.folderTrust.properties.enabled.type,
+        getSettingsSchema().security.properties.folderTrust.properties.enabled
+          .type,
       ).toBe('boolean');
       expect(
-        SETTINGS_SCHEMA.security.properties.folderTrust.properties.enabled
+        getSettingsSchema().security.properties.folderTrust.properties.enabled
           .category,
       ).toBe('Security');
       expect(
-        SETTINGS_SCHEMA.security.properties.folderTrust.properties.enabled
+        getSettingsSchema().security.properties.folderTrust.properties.enabled
           .default,
       ).toBe(false);
       expect(
-        SETTINGS_SCHEMA.security.properties.folderTrust.properties.enabled
+        getSettingsSchema().security.properties.folderTrust.properties.enabled
           .showInDialog,
       ).toBe(true);
     });
 
     it('should have debugKeystrokeLogging setting in schema', () => {
       expect(
-        SETTINGS_SCHEMA.general.properties.debugKeystrokeLogging,
+        getSettingsSchema().general.properties.debugKeystrokeLogging,
       ).toBeDefined();
       expect(
-        SETTINGS_SCHEMA.general.properties.debugKeystrokeLogging.type,
+        getSettingsSchema().general.properties.debugKeystrokeLogging.type,
       ).toBe('boolean');
       expect(
-        SETTINGS_SCHEMA.general.properties.debugKeystrokeLogging.category,
+        getSettingsSchema().general.properties.debugKeystrokeLogging.category,
       ).toBe('General');
       expect(
-        SETTINGS_SCHEMA.general.properties.debugKeystrokeLogging.default,
+        getSettingsSchema().general.properties.debugKeystrokeLogging.default,
       ).toBe(false);
       expect(
-        SETTINGS_SCHEMA.general.properties.debugKeystrokeLogging
+        getSettingsSchema().general.properties.debugKeystrokeLogging
           .requiresRestart,
       ).toBe(false);
       expect(
-        SETTINGS_SCHEMA.general.properties.debugKeystrokeLogging.showInDialog,
+        getSettingsSchema().general.properties.debugKeystrokeLogging
+          .showInDialog,
       ).toBe(true);
       expect(
-        SETTINGS_SCHEMA.general.properties.debugKeystrokeLogging.description,
+        getSettingsSchema().general.properties.debugKeystrokeLogging
+          .description,
       ).toBe('Enable debug logging of keystrokes to the console.');
     });
   });

packages/cli/src/config/settingsSchema.ts

@@ -11,20 +11,69 @@ import type {
   AuthType,
   ChatCompressionSettings,
 } from '@google/gemini-cli-core';
+import {
+  DEFAULT_TRUNCATE_TOOL_OUTPUT_LINES,
+  DEFAULT_TRUNCATE_TOOL_OUTPUT_THRESHOLD,
+} from '@google/gemini-cli-core';
 import type { CustomTheme } from '../ui/themes/theme.js';
 
+export type SettingsType =
+  | 'boolean'
+  | 'string'
+  | 'number'
+  | 'array'
+  | 'object'
+  | 'enum';
+
+export type SettingsValue =
+  | boolean
+  | string
+  | number
+  | string[]
+  | object
+  | undefined;
+
+/**
+ * Setting datatypes that "toggle" through a fixed list of options
+ * (e.g. an enum or true/false) rather than allowing for free form input
+ * (like a number or string).
+ */
+export const TOGGLE_TYPES: ReadonlySet<SettingsType | undefined> = new Set([
+  'boolean',
+  'enum',
+]);
+
+export interface SettingEnumOption {
+  value: string | number;
+  label: string;
+}
+
+export enum MergeStrategy {
+  // Replace the old value with the new value. This is the default.
+  REPLACE = 'replace',
+  // Concatenate arrays.
+  CONCAT = 'concat',
+  // Merge arrays, ensuring unique values.
+  UNION = 'union',
+  // Shallow merge objects.
+  SHALLOW_MERGE = 'shallow_merge',
+}
+
 export interface SettingDefinition {
-  type: 'boolean' | 'string' | 'number' | 'array' | 'object';
+  type: SettingsType;
   label: string;
   category: string;
   requiresRestart: boolean;
-  default: boolean | string | number | string[] | object | undefined;
+  default: SettingsValue;
   description?: string;
   parentKey?: string;
   childKey?: string;
   key?: string;
   properties?: SettingsSchema;
   showInDialog?: boolean;
+  mergeStrategy?: MergeStrategy;
+  /** Enum type options  */
+  options?: readonly SettingEnumOption[];
 }
 
 export interface SettingsSchema {
@@ -39,7 +88,7 @@ export type DnsResolutionOrder = 'ipv4first' | 'verbatim';
  * The structure of this object defines the structure of the `Settings` type.
  * `as const` is crucial for TypeScript to infer the most specific types possible.
  */
-export const SETTINGS_SCHEMA = {
+const SETTINGS_SCHEMA = {
   // Maintained for compatibility/criticality
   mcpServers: {
     type: 'object',
@@ -49,6 +98,7 @@ export const SETTINGS_SCHEMA = {
     default: {} as Record<string, MCPServerConfig>,
     description: 'Configuration for MCP servers.',
     showInDialog: false,
+    mergeStrategy: MergeStrategy.SHALLOW_MERGE,
   },
 
   general: {
@@ -192,6 +242,55 @@ export const SETTINGS_SCHEMA = {
         description: 'Hide the application banner',
         showInDialog: true,
       },
+      hideContextSummary: {
+        type: 'boolean',
+        label: 'Hide Context Summary',
+        category: 'UI',
+        requiresRestart: false,
+        default: false,
+        description:
+          'Hide the context summary (GEMINI.md, MCP servers) above the input.',
+        showInDialog: true,
+      },
+      footer: {
+        type: 'object',
+        label: 'Footer',
+        category: 'UI',
+        requiresRestart: false,
+        default: {},
+        description: 'Settings for the footer.',
+        showInDialog: false,
+        properties: {
+          hideCWD: {
+            type: 'boolean',
+            label: 'Hide CWD',
+            category: 'UI',
+            requiresRestart: false,
+            default: false,
+            description:
+              'Hide the current working directory path in the footer.',
+            showInDialog: true,
+          },
+          hideSandboxStatus: {
+            type: 'boolean',
+            label: 'Hide Sandbox Status',
+            category: 'UI',
+            requiresRestart: false,
+            default: false,
+            description: 'Hide the sandbox status indicator in the footer.',
+            showInDialog: true,
+          },
+          hideModelInfo: {
+            type: 'boolean',
+            label: 'Hide Model Info',
+            category: 'UI',
+            requiresRestart: false,
+            default: false,
+            description: 'Hide the model name and context usage in the footer.',
+            showInDialog: true,
+          },
+        },
+      },
       hideFooter: {
         type: 'boolean',
         label: 'Hide Footer',
@@ -219,6 +318,24 @@ export const SETTINGS_SCHEMA = {
         description: 'Show line numbers in the chat.',
         showInDialog: true,
       },
+      showCitations: {
+        type: 'boolean',
+        label: 'Show Citations',
+        category: 'UI',
+        requiresRestart: false,
+        default: false,
+        description: 'Show citations for generated text in the chat.',
+        showInDialog: true,
+      },
+      customWittyPhrases: {
+        type: 'array',
+        label: 'Custom Witty Phrases',
+        category: 'UI',
+        requiresRestart: false,
+        default: [] as string[],
+        description: 'Custom witty phrases to display during loading.',
+        showInDialog: false,
+      },
       accessibility: {
         type: 'object',
         label: 'Accessibility',
@@ -366,7 +483,7 @@ export const SETTINGS_SCHEMA = {
         label: 'Skip Next Speaker Check',
         category: 'Model',
         requiresRestart: false,
-        default: false,
+        default: true,
         description: 'Skip the next speaker check.',
         showInDialog: true,
       },
@@ -418,6 +535,7 @@ export const SETTINGS_SCHEMA = {
         description:
           'Additional directories to include in the workspace context. Missing directories will be skipped with a warning.',
         showInDialog: false,
+        mergeStrategy: MergeStrategy.CONCAT,
       },
       loadMemoryFromIncludeDirectories: {
         type: 'boolean',
@@ -507,6 +625,16 @@ export const SETTINGS_SCHEMA = {
           'Use node-pty for shell command execution. Fallback to child_process still applies.',
         showInDialog: true,
       },
+      autoAccept: {
+        type: 'boolean',
+        label: 'Auto Accept',
+        category: 'Tools',
+        requiresRestart: false,
+        default: false,
+        description:
+          'Automatically accept and execute tool calls that are considered safe (e.g., read-only operations).',
+        showInDialog: true,
+      },
       core: {
         type: 'array',
         label: 'Core Tools',
@@ -563,6 +691,34 @@ export const SETTINGS_SCHEMA = {
           'Use ripgrep for file content search instead of the fallback implementation. Provides faster search performance.',
         showInDialog: true,
       },
+      enableToolOutputTruncation: {
+        type: 'boolean',
+        label: 'Enable Tool Output Truncation',
+        category: 'General',
+        requiresRestart: true,
+        default: false,
+        description: 'Enable truncation of large tool outputs.',
+        showInDialog: true,
+      },
+      truncateToolOutputThreshold: {
+        type: 'number',
+        label: 'Tool Output Truncation Threshold',
+        category: 'General',
+        requiresRestart: true,
+        default: DEFAULT_TRUNCATE_TOOL_OUTPUT_THRESHOLD,
+        description:
+          'Truncate tool output if it is larger than this many characters. Set to -1 to disable.',
+        showInDialog: true,
+      },
+      truncateToolOutputLines: {
+        type: 'number',
+        label: 'Tool Output Truncation Lines',
+        category: 'General',
+        requiresRestart: true,
+        default: DEFAULT_TRUNCATE_TOOL_OUTPUT_LINES,
+        description: 'The number of lines to keep when truncating tool output.',
+        showInDialog: true,
+      },
     },
   },
 
@@ -590,7 +746,7 @@ export const SETTINGS_SCHEMA = {
         category: 'MCP',
         requiresRestart: true,
         default: undefined as string[] | undefined,
-        description: 'A whitelist of MCP servers to allow.',
+        description: 'A list of MCP servers to allow.',
         showInDialog: false,
       },
       excluded: {
@@ -599,12 +755,20 @@ export const SETTINGS_SCHEMA = {
         category: 'MCP',
         requiresRestart: true,
         default: undefined as string[] | undefined,
-        description: 'A blacklist of MCP servers to exclude.',
+        description: 'A list of MCP servers to exclude.',
         showInDialog: false,
       },
     },
   },
-
+  useSmartEdit: {
+    type: 'boolean',
+    label: 'Use Smart Edit',
+    category: 'Advanced',
+    requiresRestart: false,
+    default: false,
+    description: 'Enable the smart-edit tool instead of the replace tool.',
+    showInDialog: false,
+  },
   security: {
     type: 'object',
     label: 'Security',
@@ -623,20 +787,11 @@ export const SETTINGS_SCHEMA = {
         description: 'Settings for folder trust.',
         showInDialog: false,
         properties: {
-          featureEnabled: {
-            type: 'boolean',
-            label: 'Folder Trust Feature',
-            category: 'Security',
-            requiresRestart: false,
-            default: false,
-            description: 'Enable folder trust feature for enhanced security.',
-            showInDialog: true,
-          },
           enabled: {
             type: 'boolean',
             label: 'Folder Trust',
             category: 'Security',
-            requiresRestart: false,
+            requiresRestart: true,
             default: false,
             description: 'Setting to track whether Folder trust is enabled.',
             showInDialog: true,
@@ -661,6 +816,16 @@ export const SETTINGS_SCHEMA = {
             description: 'The currently selected authentication type.',
             showInDialog: false,
           },
+          enforcedType: {
+            type: 'string',
+            label: 'Enforced Auth Type',
+            category: 'Advanced',
+            requiresRestart: true,
+            default: undefined as AuthType | undefined,
+            description:
+              'The required auth type. If this does not match the selected auth type, the user will be prompted to re-authenticate.',
+            showInDialog: false,
+          },
           useExternal: {
             type: 'boolean',
             label: 'Use External Auth',
@@ -710,6 +875,7 @@ export const SETTINGS_SCHEMA = {
         default: ['DEBUG', 'DEBUG_MODE'] as string[],
         description: 'Environment variables to exclude from project context.',
         showInDialog: false,
+        mergeStrategy: MergeStrategy.UNION,
       },
       bugCommand: {
         type: 'object',
@@ -737,7 +903,7 @@ export const SETTINGS_SCHEMA = {
         label: 'Extension Management',
         category: 'Experimental',
         requiresRestart: true,
-        default: false,
+        default: true,
         description: 'Enable extension management features.',
         showInDialog: false,
       },
@@ -761,6 +927,7 @@ export const SETTINGS_SCHEMA = {
         default: [] as string[],
         description: 'List of disabled extensions.',
         showInDialog: false,
+        mergeStrategy: MergeStrategy.UNION,
       },
       workspacesWithMigrationNudge: {
         type: 'array',
@@ -771,10 +938,17 @@ export const SETTINGS_SCHEMA = {
         description:
           'List of workspaces for which the migration nudge has been shown.',
         showInDialog: false,
+        mergeStrategy: MergeStrategy.UNION,
       },
     },
   },
-} as const;
+} as const satisfies SettingsSchema;
+
+export type SettingsSchemaType = typeof SETTINGS_SCHEMA;
+
+export function getSettingsSchema(): SettingsSchemaType {
+  return SETTINGS_SCHEMA;
+}
 
 type InferSettings<T extends SettingsSchema> = {
   -readonly [K in keyof T]?: T[K] extends { properties: SettingsSchema }
@@ -784,4 +958,10 @@ type InferSettings<T extends SettingsSchema> = {
       : T[K]['default'];
 };
 
-export type Settings = InferSettings<typeof SETTINGS_SCHEMA>;
+export type Settings = InferSettings<SettingsSchemaType>;
+
+export interface FooterSettings {
+  hideCWD?: boolean;
+  hideSandboxStatus?: boolean;
+  hideModelInfo?: boolean;
+}

packages/cli/src/config/trustedFolders.test.ts

@@ -80,6 +80,52 @@ describe('Trusted Folders Loading', () => {
     expect(errors).toEqual([]);
   });
 
+  describe('isPathTrusted', () => {
+    function setup({ config = {} as Record<string, TrustLevel> } = {}) {
+      (mockFsExistsSync as Mock).mockImplementation(
+        (p) => p === USER_TRUSTED_FOLDERS_PATH,
+      );
+      (fs.readFileSync as Mock).mockImplementation((p) => {
+        if (p === USER_TRUSTED_FOLDERS_PATH) return JSON.stringify(config);
+        return '{}';
+      });
+
+      const folders = loadTrustedFolders();
+
+      return { folders };
+    }
+
+    it('provides a method to determine if a path is trusted', () => {
+      const { folders } = setup({
+        config: {
+          './myfolder': TrustLevel.TRUST_FOLDER,
+          '/trustedparent/trustme': TrustLevel.TRUST_PARENT,
+          '/user/folder': TrustLevel.TRUST_FOLDER,
+          '/secret': TrustLevel.DO_NOT_TRUST,
+          '/secret/publickeys': TrustLevel.TRUST_FOLDER,
+        },
+      });
+      expect(folders.isPathTrusted('/secret')).toBe(false);
+      expect(folders.isPathTrusted('/user/folder')).toBe(true);
+      expect(folders.isPathTrusted('/secret/publickeys/public.pem')).toBe(true);
+      expect(folders.isPathTrusted('/user/folder/harhar')).toBe(true);
+      expect(folders.isPathTrusted('myfolder/somefile.jpg')).toBe(true);
+      expect(folders.isPathTrusted('/trustedparent/someotherfolder')).toBe(
+        true,
+      );
+      expect(folders.isPathTrusted('/trustedparent/trustme')).toBe(true);
+
+      // No explicit rule covers this file
+      expect(folders.isPathTrusted('/secret/bankaccounts.json')).toBe(
+        undefined,
+      );
+      expect(folders.isPathTrusted('/secret/mine/privatekey.pem')).toBe(
+        undefined,
+      );
+      expect(folders.isPathTrusted('/user/someotherfolder')).toBe(undefined);
+    });
+  });
+
   it('should load user rules if only user file exists', () => {
     const userPath = USER_TRUSTED_FOLDERS_PATH;
     (mockFsExistsSync as Mock).mockImplementation((p) => p === userPath);
@@ -123,7 +169,7 @@ describe('Trusted Folders Loading', () => {
     expect(mockFsWriteFileSync).toHaveBeenCalledWith(
       USER_TRUSTED_FOLDERS_PATH,
       JSON.stringify({ '/new/path': TrustLevel.TRUST_FOLDER }, null, 2),
-      'utf-8',
+      { encoding: 'utf-8', mode: 0o600 },
     );
   });
 });
@@ -134,7 +180,6 @@ describe('isWorkspaceTrusted', () => {
   const mockSettings: Settings = {
     security: {
       folderTrust: {
-        featureEnabled: true,
         enabled: true,
       },
     },
@@ -210,3 +255,62 @@ describe('isWorkspaceTrusted', () => {
     expect(isWorkspaceTrusted(mockSettings)).toBe(true);
   });
 });
+
+import { getIdeTrust } from '@google/gemini-cli-core';
+
+vi.mock('@google/gemini-cli-core', async (importOriginal) => {
+  const actual = await importOriginal<Record<string, unknown>>();
+  return {
+    ...actual,
+    getIdeTrust: vi.fn(),
+  };
+});
+
+describe('isWorkspaceTrusted with IDE override', () => {
+  const mockSettings: Settings = {
+    security: {
+      folderTrust: {
+        enabled: true,
+      },
+    },
+  };
+
+  it('should return true when ideTrust is true, ignoring config', () => {
+    vi.mocked(getIdeTrust).mockReturnValue(true);
+    // Even if config says don't trust, ideTrust should win.
+    vi.spyOn(fs, 'readFileSync').mockReturnValue(
+      JSON.stringify({ [process.cwd()]: TrustLevel.DO_NOT_TRUST }),
+    );
+    expect(isWorkspaceTrusted(mockSettings)).toBe(true);
+  });
+
+  it('should return false when ideTrust is false, ignoring config', () => {
+    vi.mocked(getIdeTrust).mockReturnValue(false);
+    // Even if config says trust, ideTrust should win.
+    vi.spyOn(fs, 'readFileSync').mockReturnValue(
+      JSON.stringify({ [process.cwd()]: TrustLevel.TRUST_FOLDER }),
+    );
+    expect(isWorkspaceTrusted(mockSettings)).toBe(false);
+  });
+
+  it('should fall back to config when ideTrust is undefined', () => {
+    vi.mocked(getIdeTrust).mockReturnValue(undefined);
+    vi.spyOn(fs, 'existsSync').mockReturnValue(true);
+    vi.spyOn(fs, 'readFileSync').mockReturnValue(
+      JSON.stringify({ [process.cwd()]: TrustLevel.TRUST_FOLDER }),
+    );
+    expect(isWorkspaceTrusted(mockSettings)).toBe(true);
+  });
+
+  it('should always return true if folderTrust setting is disabled', () => {
+    const settings: Settings = {
+      security: {
+        folderTrust: {
+          enabled: false,
+        },
+      },
+    };
+    vi.mocked(getIdeTrust).mockReturnValue(false);
+    expect(isWorkspaceTrusted(settings)).toBe(true);
+  });
+});

packages/cli/src/config/trustedFolders.ts

@@ -7,7 +7,11 @@
 import * as fs from 'node:fs';
 import * as path from 'node:path';
 import { homedir } from 'node:os';
-import { getErrorMessage, isWithinRoot } from '@google/gemini-cli-core';
+import {
+  getErrorMessage,
+  isWithinRoot,
+  getIdeTrust,
+} from '@google/gemini-cli-core';
 import type { Settings } from './settings.js';
 import stripJsonComments from 'strip-json-comments';
 
@@ -42,8 +46,8 @@ export interface TrustedFoldersFile {
 
 export class LoadedTrustedFolders {
   constructor(
-    public user: TrustedFoldersFile,
-    public errors: TrustedFoldersError[],
+    readonly user: TrustedFoldersFile,
+    readonly errors: TrustedFoldersError[],
   ) {}
 
   get rules(): TrustRule[] {
@@ -53,6 +57,49 @@ export class LoadedTrustedFolders {
     }));
   }
 
+  /**
+   * Returns true or false if the path should be "trusted". This function
+   * should only be invoked when the folder trust setting is active.
+   *
+   * @param location path
+   * @returns
+   */
+  isPathTrusted(location: string): boolean | undefined {
+    const trustedPaths: string[] = [];
+    const untrustedPaths: string[] = [];
+
+    for (const rule of this.rules) {
+      switch (rule.trustLevel) {
+        case TrustLevel.TRUST_FOLDER:
+          trustedPaths.push(rule.path);
+          break;
+        case TrustLevel.TRUST_PARENT:
+          trustedPaths.push(path.dirname(rule.path));
+          break;
+        case TrustLevel.DO_NOT_TRUST:
+          untrustedPaths.push(rule.path);
+          break;
+        default:
+          // Do nothing for unknown trust levels.
+          break;
+      }
+    }
+
+    for (const trustedPath of trustedPaths) {
+      if (isWithinRoot(location, trustedPath)) {
+        return true;
+      }
+    }
+
+    for (const untrustedPath of untrustedPaths) {
+      if (path.normalize(location) === path.normalize(untrustedPath)) {
+        return false;
+      }
+    }
+
+    return undefined;
+  }
+
   setValue(path: string, trustLevel: TrustLevel): void {
     this.user.config[path] = trustLevel;
     saveTrustedFolders(this.user);
@@ -103,66 +150,43 @@ export function saveTrustedFolders(
     fs.writeFileSync(
       trustedFoldersFile.path,
       JSON.stringify(trustedFoldersFile.config, null, 2),
-      'utf-8',
+      { encoding: 'utf-8', mode: 0o600 },
     );
   } catch (error) {
     console.error('Error saving trusted folders file:', error);
   }
 }
 
-export function isWorkspaceTrusted(settings: Settings): boolean | undefined {
-  const folderTrustFeature =
-    settings.security?.folderTrust?.featureEnabled ?? false;
-  const folderTrustSetting = settings.security?.folderTrust?.enabled ?? true;
-  const folderTrustEnabled = folderTrustFeature && folderTrustSetting;
+/** Is folder trust feature enabled per the current applied settings */
+export function isFolderTrustEnabled(settings: Settings): boolean {
+  const folderTrustSetting = settings.security?.folderTrust?.enabled ?? false;
+  return folderTrustSetting;
+}
 
-  if (!folderTrustEnabled) {
-    return true;
-  }
+function getWorkspaceTrustFromLocalConfig(): boolean | undefined {
+  const folders = loadTrustedFolders();
 
-  const { rules, errors } = loadTrustedFolders();
-
-  if (errors.length > 0) {
-    for (const error of errors) {
+  if (folders.errors.length > 0) {
+    for (const error of folders.errors) {
       console.error(
         `Error loading trusted folders config from ${error.path}: ${error.message}`,
       );
     }
   }
 
-  const trustedPaths: string[] = [];
-  const untrustedPaths: string[] = [];
-
-  for (const rule of rules) {
-    switch (rule.trustLevel) {
-      case TrustLevel.TRUST_FOLDER:
-        trustedPaths.push(rule.path);
-        break;
-      case TrustLevel.TRUST_PARENT:
-        trustedPaths.push(path.dirname(rule.path));
-        break;
-      case TrustLevel.DO_NOT_TRUST:
-        untrustedPaths.push(rule.path);
-        break;
-      default:
-        // Do nothing for unknown trust levels.
-        break;
-    }
-  }
-
-  const cwd = process.cwd();
-
-  for (const trustedPath of trustedPaths) {
-    if (isWithinRoot(cwd, trustedPath)) {
-      return true;
-    }
-  }
-
-  for (const untrustedPath of untrustedPaths) {
-    if (path.normalize(cwd) === path.normalize(untrustedPath)) {
-      return false;
-    }
-  }
-
-  return undefined;
+  return folders.isPathTrusted(process.cwd());
+}
+
+export function isWorkspaceTrusted(settings: Settings): boolean | undefined {
+  if (!isFolderTrustEnabled(settings)) {
+    return true;
+  }
+
+  const ideTrust = getIdeTrust();
+  if (ideTrust !== undefined) {
+    return ideTrust;
+  }
+
+  // Fall back to the local user configuration
+  return getWorkspaceTrustFromLocalConfig();
 }

packages/cli/src/core/auth.ts

@@ -0,0 +1,36 @@
+/**
+ * @license
+ * Copyright 2025 Google LLC
+ * SPDX-License-Identifier: Apache-2.0
+ */
+
+import {
+  type AuthType,
+  type Config,
+  getErrorMessage,
+} from '@google/gemini-cli-core';
+
+/**
+ * Handles the initial authentication flow.
+ * @param config The application config.
+ * @param authType The selected auth type.
+ * @returns An error message if authentication fails, otherwise null.
+ */
+export async function performInitialAuth(
+  config: Config,
+  authType: AuthType | undefined,
+): Promise<string | null> {
+  if (!authType) {
+    return null;
+  }
+
+  try {
+    await config.refreshAuth(authType);
+    // The console.log is intentionally left out here.
+    // We can add a dedicated startup message later if needed.
+  } catch (e) {
+    return `Failed to login. Message: ${getErrorMessage(e)}`;
+  }
+
+  return null;
+}

packages/cli/src/core/initializer.ts

@@ -0,0 +1,45 @@
+/**
+ * @license
+ * Copyright 2025 Google LLC
+ * SPDX-License-Identifier: Apache-2.0
+ */
+
+import { type Config } from '@google/gemini-cli-core';
+import { type LoadedSettings } from '../config/settings.js';
+import { performInitialAuth } from './auth.js';
+import { validateTheme } from './theme.js';
+
+export interface InitializationResult {
+  authError: string | null;
+  themeError: string | null;
+  shouldOpenAuthDialog: boolean;
+  geminiMdFileCount: number;
+}
+
+/**
+ * Orchestrates the application's startup initialization.
+ * This runs BEFORE the React UI is rendered.
+ * @param config The application config.
+ * @param settings The loaded application settings.
+ * @returns The results of the initialization.
+ */
+export async function initializeApp(
+  config: Config,
+  settings: LoadedSettings,
+): Promise<InitializationResult> {
+  const authError = await performInitialAuth(
+    config,
+    settings.merged.security?.auth?.selectedType,
+  );
+  const themeError = validateTheme(settings);
+
+  const shouldOpenAuthDialog =
+    settings.merged.security?.auth?.selectedType === undefined || !!authError;
+
+  return {
+    authError,
+    themeError,
+    shouldOpenAuthDialog,
+    geminiMdFileCount: config.getGeminiMdFileCount(),
+  };
+}

packages/cli/src/core/theme.ts

@@ -0,0 +1,21 @@
+/**
+ * @license
+ * Copyright 2025 Google LLC
+ * SPDX-License-Identifier: Apache-2.0
+ */
+
+import { themeManager } from '../ui/themes/theme-manager.js';
+import { type LoadedSettings } from '../config/settings.js';
+
+/**
+ * Validates the configured theme.
+ * @param settings The loaded application settings.
+ * @returns An error message if the theme is not found, otherwise null.
+ */
+export function validateTheme(settings: LoadedSettings): string | null {
+  const effectiveTheme = settings.merged.ui?.theme;
+  if (effectiveTheme && !themeManager.findThemeByName(effectiveTheme)) {
+    return `Theme "${effectiveTheme}" not found.`;
+  }
+  return null;
+}

packages/cli/src/gemini.test.tsx

@@ -4,18 +4,24 @@
  * SPDX-License-Identifier: Apache-2.0
  */
 
-import { describe, it, expect, vi, beforeEach, afterEach } from 'vitest';
+import {
+  describe,
+  it,
+  expect,
+  vi,
+  beforeEach,
+  afterEach,
+  type MockInstance,
+} from 'vitest';
 import {
   main,
   setupUnhandledRejectionHandler,
   validateDnsResolutionOrder,
   startInteractiveUI,
 } from './gemini.js';
-import type { SettingsFile } from './config/settings.js';
-import { LoadedSettings, loadSettings } from './config/settings.js';
+import { type LoadedSettings } from './config/settings.js';
 import { appEvents, AppEvent } from './utils/events.js';
 import type { Config } from '@google/gemini-cli-core';
-import { FatalConfigError } from '@google/gemini-cli-core';
 
 // Custom error to identify mock process.exit calls
 class MockProcessExitError extends Error {
@@ -36,14 +42,10 @@ vi.mock('./config/settings.js', async (importOriginal) => {
 
 vi.mock('./config/config.js', () => ({
   loadCliConfig: vi.fn().mockResolvedValue({
-    config: {
-      getSandbox: vi.fn(() => false),
-      getQuestion: vi.fn(() => ''),
-    },
-    modelWasSwitched: false,
-    originalModelBeforeSwitch: null,
-    finalModel: 'test-model',
-  }),
+    getSandbox: vi.fn(() => false),
+    getQuestion: vi.fn(() => ''),
+  } as unknown as Config),
+  parseArguments: vi.fn().mockResolvedValue({ sessionSummary: null }),
 }));
 
 vi.mock('read-package-up', () => ({
@@ -75,7 +77,6 @@ vi.mock('./utils/sandbox.js', () => ({
 }));
 
 describe('gemini.tsx main function', () => {
-  let loadSettingsMock: ReturnType<typeof vi.mocked<typeof loadSettings>>;
   let originalEnvGeminiSandbox: string | undefined;
   let originalEnvSandbox: string | undefined;
   let initialUnhandledRejectionListeners: NodeJS.UnhandledRejectionListener[] =
@@ -88,8 +89,6 @@ describe('gemini.tsx main function', () => {
     });
 
   beforeEach(() => {
-    loadSettingsMock = vi.mocked(loadSettings);
-
     // Store and clear sandbox-related env variables to ensure a consistent test environment
     originalEnvGeminiSandbox = process.env['GEMINI_SANDBOX'];
     originalEnvSandbox = process.env['SANDBOX'];
@@ -124,42 +123,6 @@ describe('gemini.tsx main function', () => {
     vi.restoreAllMocks();
   });
 
-  it('should throw InvalidConfigurationError if settings have errors', async () => {
-    const settingsError = {
-      message: 'Test settings error',
-      path: '/test/settings.json',
-    };
-    const userSettingsFile: SettingsFile = {
-      path: '/user/settings.json',
-      settings: {},
-    };
-    const workspaceSettingsFile: SettingsFile = {
-      path: '/workspace/.gemini/settings.json',
-      settings: {},
-    };
-    const systemSettingsFile: SettingsFile = {
-      path: '/system/settings.json',
-      settings: {},
-    };
-    const systemDefaultsFile: SettingsFile = {
-      path: '/system/system-defaults.json',
-      settings: {},
-    };
-    const mockLoadedSettings = new LoadedSettings(
-      systemSettingsFile,
-      systemDefaultsFile,
-      userSettingsFile,
-      workspaceSettingsFile,
-      [settingsError],
-      true,
-      new Set(),
-    );
-
-    loadSettingsMock.mockReturnValue(mockLoadedSettings);
-
-    await expect(main()).rejects.toThrow(FatalConfigError);
-  });
-
   it('should log unhandled promise rejections and open debug console on first error', async () => {
     const appEventsMock = vi.mocked(appEvents);
     const rejectionError = new Error('Test unhandled rejection');
@@ -199,6 +162,88 @@ describe('gemini.tsx main function', () => {
   });
 });
 
+describe('gemini.tsx main function kitty protocol', () => {
+  let setRawModeSpy: MockInstance<
+    (mode: boolean) => NodeJS.ReadStream & { fd: 0 }
+  >;
+
+  beforeEach(() => {
+    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+    if (!(process.stdin as any).setRawMode) {
+      // eslint-disable-next-line @typescript-eslint/no-explicit-any
+      (process.stdin as any).setRawMode = vi.fn();
+    }
+    setRawModeSpy = vi.spyOn(process.stdin, 'setRawMode');
+  });
+
+  it('should call setRawMode and detectAndEnableKittyProtocol when isInteractive is true', async () => {
+    const { detectAndEnableKittyProtocol } = await import(
+      './ui/utils/kittyProtocolDetector.js'
+    );
+    const { loadCliConfig, parseArguments } = await import(
+      './config/config.js'
+    );
+    const { loadSettings } = await import('./config/settings.js');
+    vi.mocked(loadCliConfig).mockResolvedValue({
+      isInteractive: () => true,
+      getQuestion: () => '',
+      getSandbox: () => false,
+      getDebugMode: () => false,
+      getListExtensions: () => false,
+      getMcpServers: () => ({}),
+      initialize: vi.fn(),
+      getIdeMode: () => false,
+      getExperimentalZedIntegration: () => false,
+      getScreenReader: () => false,
+      getGeminiMdFileCount: () => 0,
+    } as unknown as Config);
+    vi.mocked(loadSettings).mockReturnValue({
+      errors: [],
+      merged: {
+        advanced: {},
+        security: { auth: {} },
+        ui: {},
+      },
+      setValue: vi.fn(),
+    } as never);
+    vi.mocked(parseArguments).mockResolvedValue({
+      model: undefined,
+      sandbox: undefined,
+      sandboxImage: undefined,
+      debug: undefined,
+      prompt: undefined,
+      promptInteractive: undefined,
+      allFiles: undefined,
+      showMemoryUsage: undefined,
+      yolo: undefined,
+      approvalMode: undefined,
+      telemetry: undefined,
+      checkpointing: undefined,
+      telemetryTarget: undefined,
+      telemetryOtlpEndpoint: undefined,
+      telemetryOtlpProtocol: undefined,
+      telemetryLogPrompts: undefined,
+      telemetryOutfile: undefined,
+      allowedMcpServerNames: undefined,
+      allowedTools: undefined,
+      experimentalAcp: undefined,
+      extensions: undefined,
+      listExtensions: undefined,
+      proxy: undefined,
+      includeDirectories: undefined,
+      screenReader: undefined,
+      useSmartEdit: undefined,
+      sessionSummary: undefined,
+      promptWords: undefined,
+    });
+
+    await main();
+
+    expect(setRawModeSpy).toHaveBeenCalledWith(true);
+    expect(detectAndEnableKittyProtocol).toHaveBeenCalledTimes(1);
+  });
+});
+
 describe('validateDnsResolutionOrder', () => {
   let consoleWarnSpy: ReturnType<typeof vi.spyOn>;
 
@@ -255,7 +300,7 @@ describe('startInteractiveUI', () => {
   }));
 
   vi.mock('./ui/utils/kittyProtocolDetector.js', () => ({
-    detectAndEnableKittyProtocol: vi.fn(() => Promise.resolve()),
+    detectAndEnableKittyProtocol: vi.fn(() => Promise.resolve(true)),
   }));
 
   vi.mock('./ui/utils/updateCheck.js', () => ({
@@ -279,11 +324,19 @@ describe('startInteractiveUI', () => {
     const { render } = await import('ink');
     const renderSpy = vi.mocked(render);
 
+    const mockInitializationResult = {
+      authError: null,
+      themeError: null,
+      shouldOpenAuthDialog: false,
+      geminiMdFileCount: 0,
+    };
+
     await startInteractiveUI(
       mockConfig,
       mockSettings,
       mockStartupWarnings,
       mockWorkspaceRoot,
+      mockInitializationResult,
     );
 
     // Verify render was called with correct options
@@ -302,22 +355,26 @@ describe('startInteractiveUI', () => {
 
   it('should perform all startup tasks in correct order', async () => {
     const { getCliVersion } = await import('./utils/version.js');
-    const { detectAndEnableKittyProtocol } = await import(
-      './ui/utils/kittyProtocolDetector.js'
-    );
     const { checkForUpdates } = await import('./ui/utils/updateCheck.js');
     const { registerCleanup } = await import('./utils/cleanup.js');
 
+    const mockInitializationResult = {
+      authError: null,
+      themeError: null,
+      shouldOpenAuthDialog: false,
+      geminiMdFileCount: 0,
+    };
+
     await startInteractiveUI(
       mockConfig,
       mockSettings,
       mockStartupWarnings,
       mockWorkspaceRoot,
+      mockInitializationResult,
     );
 
     // Verify all startup tasks were called
     expect(getCliVersion).toHaveBeenCalledTimes(1);
-    expect(detectAndEnableKittyProtocol).toHaveBeenCalledTimes(1);
     expect(registerCleanup).toHaveBeenCalledTimes(1);
 
     // Verify cleanup handler is registered with unmount function

packages/cli/src/gemini.tsx

@@ -6,7 +6,7 @@
 
 import React from 'react';
 import { render } from 'ink';
-import { AppWrapper } from './ui/App.js';
+import { AppContainer } from './ui/AppContainer.js';
 import { loadCliConfig, parseArguments } from './config/config.js';
 import { readStdin } from './utils/readStdin.js';
 import { basename } from 'node:path';
@@ -23,7 +23,11 @@ import { getUserStartupWarnings } from './utils/userStartupWarnings.js';
 import { ConsolePatcher } from './ui/utils/ConsolePatcher.js';
 import { runNonInteractive } from './nonInteractiveCli.js';
 import { loadExtensions } from './config/extension.js';
-import { cleanupCheckpoints, registerCleanup } from './utils/cleanup.js';
+import {
+  cleanupCheckpoints,
+  registerCleanup,
+  runExitCleanup,
+} from './utils/cleanup.js';
 import { getCliVersion } from './utils/version.js';
 import type { Config } from '@google/gemini-cli-core';
 import {
@@ -31,11 +35,12 @@ import {
   logUserPrompt,
   AuthType,
   getOauthClient,
-  logIdeConnection,
-  IdeConnectionEvent,
-  IdeConnectionType,
-  FatalConfigError,
+  uiTelemetryService,
 } from '@google/gemini-cli-core';
+import {
+  initializeApp,
+  type InitializationResult,
+} from './core/initializer.js';
 import { validateAuthMethod } from './config/auth.js';
 import { setMaxSizedBoxDebugging } from './ui/components/shared/MaxSizedBox.js';
 import { validateNonInteractiveAuth } from './validateNonInterActiveAuth.js';
@@ -44,6 +49,11 @@ import { checkForUpdates } from './ui/utils/updateCheck.js';
 import { handleAutoUpdate } from './utils/handleAutoUpdate.js';
 import { appEvents, AppEvent } from './utils/events.js';
 import { SettingsContext } from './ui/contexts/SettingsContext.js';
+import { writeFileSync } from 'node:fs';
+import { SessionStatsProvider } from './ui/contexts/SessionContext.js';
+import { VimModeProvider } from './ui/contexts/VimModeContext.js';
+import { KeypressProvider } from './ui/contexts/KeypressContext.js';
+import { useKittyKeyboardProtocol } from './ui/hooks/useKittyKeyboardProtocol.js';
 
 export function validateDnsResolutionOrder(
   order: string | undefined,
@@ -105,6 +115,7 @@ async function relaunchWithAdditionalArgs(additionalArgs: string[]) {
   await new Promise((resolve) => child.on('close', resolve));
   process.exit(0);
 }
+
 import { runZedIntegration } from './zed-integration/zedIntegration.js';
 
 export function setupUnhandledRejectionHandler() {
@@ -133,24 +144,46 @@ export async function startInteractiveUI(
   config: Config,
   settings: LoadedSettings,
   startupWarnings: string[],
-  workspaceRoot: string,
+  workspaceRoot: string = process.cwd(),
+  initializationResult: InitializationResult,
 ) {
   const version = await getCliVersion();
-  // Detect and enable Kitty keyboard protocol once at startup
-  await detectAndEnableKittyProtocol();
   setWindowTitle(basename(workspaceRoot), settings);
+
+  // Create wrapper component to use hooks inside render
+  const AppWrapper = () => {
+    const kittyProtocolStatus = useKittyKeyboardProtocol();
+    return (
+      <SettingsContext.Provider value={settings}>
+        <KeypressProvider
+          kittyProtocolEnabled={kittyProtocolStatus.enabled}
+          config={config}
+          debugKeystrokeLogging={settings.merged.general?.debugKeystrokeLogging}
+        >
+          <SessionStatsProvider>
+            <VimModeProvider settings={settings}>
+              <AppContainer
+                config={config}
+                settings={settings}
+                startupWarnings={startupWarnings}
+                version={version}
+                initializationResult={initializationResult}
+              />
+            </VimModeProvider>
+          </SessionStatsProvider>
+        </KeypressProvider>
+      </SettingsContext.Provider>
+    );
+  };
+
   const instance = render(
     <React.StrictMode>
-      <SettingsContext.Provider value={settings}>
-        <AppWrapper
-          config={config}
-          settings={settings}
-          startupWarnings={startupWarnings}
-          version={version}
-        />
-      </SettingsContext.Provider>
+      <AppWrapper />
     </React.StrictMode>,
-    { exitOnCtrlC: false, isScreenReaderEnabled: config.getScreenReader() },
+    {
+      exitOnCtrlC: false,
+      isScreenReaderEnabled: config.getScreenReader(),
+    },
   );
 
   checkForUpdates()
@@ -169,21 +202,12 @@ export async function startInteractiveUI(
 
 export async function main() {
   setupUnhandledRejectionHandler();
-  const workspaceRoot = process.cwd();
-  const settings = loadSettings(workspaceRoot);
+  const settings = loadSettings();
 
   await cleanupCheckpoints();
-  if (settings.errors.length > 0) {
-    const errorMessages = settings.errors.map(
-      (error) => `Error in ${error.path}: ${error.message}`,
-    );
-    throw new FatalConfigError(
-      `${errorMessages.join('\n')}\nPlease fix the configuration file(s) and try again.`,
-    );
-  }
 
   const argv = await parseArguments(settings.merged);
-  const extensions = loadExtensions(workspaceRoot);
+  const extensions = loadExtensions();
   const config = await loadCliConfig(
     settings.merged,
     extensions,
@@ -191,6 +215,34 @@ export async function main() {
     argv,
   );
 
+  const wasRaw = process.stdin.isRaw;
+  let kittyProtocolDetectionComplete: Promise<boolean> | undefined;
+  if (config.isInteractive() && !wasRaw) {
+    // Set this as early as possible to avoid spurious characters from
+    // input showing up in the output.
+    process.stdin.setRawMode(true);
+
+    // This cleanup isn't strictly needed but may help in certain situations.
+    process.on('SIGTERM', () => {
+      process.stdin.setRawMode(wasRaw);
+    });
+    process.on('SIGINT', () => {
+      process.stdin.setRawMode(wasRaw);
+    });
+
+    // Detect and enable Kitty keyboard protocol once at startup.
+    kittyProtocolDetectionComplete = detectAndEnableKittyProtocol();
+  }
+  if (argv.sessionSummary) {
+    registerCleanup(() => {
+      const metrics = uiTelemetryService.getMetrics();
+      writeFileSync(
+        argv.sessionSummary!,
+        JSON.stringify({ sessionMetrics: metrics }, null, 2),
+      );
+    });
+  }
+
   const consolePatcher = new ConsolePatcher({
     stderr: true,
     debugMode: config.getDebugMode(),
@@ -227,35 +279,22 @@ export async function main() {
       );
     }
   }
-  // Empty key causes issues with the GoogleGenAI package.
-  if (process.env['GEMINI_API_KEY']?.trim() === '') {
-    delete process.env['GEMINI_API_KEY'];
-  }
-
-  if (process.env['GOOGLE_API_KEY']?.trim() === '') {
-    delete process.env['GOOGLE_API_KEY'];
-  }
 
   setMaxSizedBoxDebugging(config.getDebugMode());
 
-  await config.initialize();
-
-  if (config.getIdeMode()) {
-    await config.getIdeClient().connect();
-    logIdeConnection(config, new IdeConnectionEvent(IdeConnectionType.START));
-  }
-
   // Load custom themes from settings
   themeManager.loadCustomThemes(settings.merged.ui?.customThemes);
 
   if (settings.merged.ui?.theme) {
     if (!themeManager.setActiveTheme(settings.merged.ui?.theme)) {
       // If the theme is not found during initial load, log a warning and continue.
-      // The useThemeCommand hook in App.tsx will handle opening the dialog.
+      // The useThemeCommand hook in AppContainer.tsx will handle opening the dialog.
       console.warn(`Warning: Theme "${settings.merged.ui?.theme}" not found.`);
     }
   }
 
+  const initializationResult = await initializeApp(config, settings);
+
   // hop into sandbox if we are outside and sandboxing is enabled
   if (!process.env['SANDBOX']) {
     const memoryArgs = settings.merged.advanced?.autoConfigureMemory
@@ -339,14 +378,25 @@ export async function main() {
   let input = config.getQuestion();
   const startupWarnings = [
     ...(await getStartupWarnings()),
-    ...(await getUserStartupWarnings(workspaceRoot)),
+    ...(await getUserStartupWarnings()),
   ];
 
   // Render UI, passing necessary config values. Check that there is no command line question.
   if (config.isInteractive()) {
-    await startInteractiveUI(config, settings, startupWarnings, workspaceRoot);
+    // Need kitty detection to be complete before we can start the interactive UI.
+    await kittyProtocolDetectionComplete;
+    await startInteractiveUI(
+      config,
+      settings,
+      startupWarnings,
+      process.cwd(),
+      initializationResult,
+    );
     return;
   }
+
+  await config.initialize();
+
   // If not a TTY, read from stdin
   // This is for cases where the user pipes input directly into the command
   if (!process.stdin.isTTY) {
@@ -376,6 +426,7 @@ export async function main() {
     settings.merged.security?.auth?.selectedType,
     settings.merged.security?.auth?.useExternal,
     config,
+    settings,
   );
 
   if (config.getDebugMode()) {
@@ -383,6 +434,8 @@ export async function main() {
   }
 
   await runNonInteractive(nonInteractiveConfig, input, prompt_id);
+  // Call cleanup before process.exit, which causes cleanup to not run
+  await runExitCleanup();
   process.exit(0);
 }
 

packages/cli/src/nonInteractiveCli.test.ts

@@ -24,11 +24,20 @@ vi.mock('./ui/hooks/atCommandProcessor.js');
 vi.mock('@google/gemini-cli-core', async (importOriginal) => {
   const original =
     await importOriginal<typeof import('@google/gemini-cli-core')>();
+
+  class MockChatRecordingService {
+    initialize = vi.fn();
+    recordMessage = vi.fn();
+    recordMessageTokens = vi.fn();
+    recordToolCalls = vi.fn();
+  }
+
   return {
     ...original,
     executeToolCall: vi.fn(),
     shutdownTelemetry: vi.fn(),
     isTelemetrySdkInitialized: vi.fn().mockReturnValue(true),
+    ChatRecordingService: MockChatRecordingService,
   };
 });
 
@@ -41,6 +50,7 @@ describe('runNonInteractive', () => {
   let processStdoutSpy: vi.SpyInstance;
   let mockGeminiClient: {
     sendMessageStream: vi.Mock;
+    getChatRecordingService: vi.Mock;
   };
 
   beforeEach(async () => {
@@ -59,6 +69,12 @@ describe('runNonInteractive', () => {
 
     mockGeminiClient = {
       sendMessageStream: vi.fn(),
+      getChatRecordingService: vi.fn(() => ({
+        initialize: vi.fn(),
+        recordMessage: vi.fn(),
+        recordMessageTokens: vi.fn(),
+        recordToolCalls: vi.fn(),
+      })),
     };
 
     mockConfig = {
@@ -66,6 +82,11 @@ describe('runNonInteractive', () => {
       getGeminiClient: vi.fn().mockReturnValue(mockGeminiClient),
       getToolRegistry: vi.fn().mockReturnValue(mockToolRegistry),
       getMaxSessionTurns: vi.fn().mockReturnValue(10),
+      getSessionId: vi.fn().mockReturnValue('test-session-id'),
+      getProjectRoot: vi.fn().mockReturnValue('/test/project'),
+      storage: {
+        getProjectTempDir: vi.fn().mockReturnValue('/test/project/.gemini/tmp'),
+      },
       getIdeMode: vi.fn().mockReturnValue(false),
       getFullContext: vi.fn().mockReturnValue(false),
       getContentGeneratorConfig: vi.fn().mockReturnValue({}),
@@ -97,6 +118,10 @@ describe('runNonInteractive', () => {
     const events: ServerGeminiStreamEvent[] = [
       { type: GeminiEventType.Content, value: 'Hello' },
       { type: GeminiEventType.Content, value: ' World' },
+      {
+        type: GeminiEventType.Finished,
+        value: { reason: undefined, usageMetadata: { totalTokenCount: 10 } },
+      },
     ];
     mockGeminiClient.sendMessageStream.mockReturnValue(
       createStreamFromEvents(events),
@@ -132,6 +157,10 @@ describe('runNonInteractive', () => {
     const firstCallEvents: ServerGeminiStreamEvent[] = [toolCallEvent];
     const secondCallEvents: ServerGeminiStreamEvent[] = [
       { type: GeminiEventType.Content, value: 'Final answer' },
+      {
+        type: GeminiEventType.Finished,
+        value: { reason: undefined, usageMetadata: { totalTokenCount: 10 } },
+      },
     ];
 
     mockGeminiClient.sendMessageStream
@@ -187,6 +216,10 @@ describe('runNonInteractive', () => {
         type: GeminiEventType.Content,
         value: 'Sorry, let me try again.',
       },
+      {
+        type: GeminiEventType.Finished,
+        value: { reason: undefined, usageMetadata: { totalTokenCount: 10 } },
+      },
     ];
     mockGeminiClient.sendMessageStream
       .mockReturnValueOnce(createStreamFromEvents([toolCallEvent]))
@@ -242,12 +275,17 @@ describe('runNonInteractive', () => {
     mockCoreExecuteToolCall.mockResolvedValue({
       error: new Error('Tool "nonexistentTool" not found in registry.'),
       resultDisplay: 'Tool "nonexistentTool" not found in registry.',
+      responseParts: [],
     });
     const finalResponse: ServerGeminiStreamEvent[] = [
       {
         type: GeminiEventType.Content,
         value: "Sorry, I can't find that tool.",
       },
+      {
+        type: GeminiEventType.Finished,
+        value: { reason: undefined, usageMetadata: { totalTokenCount: 10 } },
+      },
     ];
 
     mockGeminiClient.sendMessageStream
@@ -304,6 +342,10 @@ describe('runNonInteractive', () => {
     // Mock a simple stream response from the Gemini client
     const events: ServerGeminiStreamEvent[] = [
       { type: GeminiEventType.Content, value: 'Summary complete.' },
+      {
+        type: GeminiEventType.Finished,
+        value: { reason: undefined, usageMetadata: { totalTokenCount: 10 } },
+      },
     ];
     mockGeminiClient.sendMessageStream.mockReturnValue(
       createStreamFromEvents(events),

packages/cli/src/nonInteractiveCli.ts

@@ -13,6 +13,7 @@ import {
   parseAndFormatApiError,
   FatalInputError,
   FatalTurnLimitedError,
+  promptIdContext,
 } from '@google/gemini-cli-core';
 import type { Content, Part } from '@google/genai';
 
@@ -24,115 +25,117 @@ export async function runNonInteractive(
   input: string,
   prompt_id: string,
 ): Promise<void> {
-  const consolePatcher = new ConsolePatcher({
-    stderr: true,
-    debugMode: config.getDebugMode(),
-  });
-
-  try {
-    consolePatcher.patch();
-    // Handle EPIPE errors when the output is piped to a command that closes early.
-    process.stdout.on('error', (err: NodeJS.ErrnoException) => {
-      if (err.code === 'EPIPE') {
-        // Exit gracefully if the pipe is closed.
-        process.exit(0);
-      }
+  return promptIdContext.run(prompt_id, async () => {
+    const consolePatcher = new ConsolePatcher({
+      stderr: true,
+      debugMode: config.getDebugMode(),
     });
 
-    const geminiClient = config.getGeminiClient();
+    try {
+      consolePatcher.patch();
+      // Handle EPIPE errors when the output is piped to a command that closes early.
+      process.stdout.on('error', (err: NodeJS.ErrnoException) => {
+        if (err.code === 'EPIPE') {
+          // Exit gracefully if the pipe is closed.
+          process.exit(0);
+        }
+      });
 
-    const abortController = new AbortController();
+      const geminiClient = config.getGeminiClient();
 
-    const { processedQuery, shouldProceed } = await handleAtCommand({
-      query: input,
-      config,
-      addItem: (_item, _timestamp) => 0,
-      onDebugMessage: () => {},
-      messageId: Date.now(),
-      signal: abortController.signal,
-    });
+      const abortController = new AbortController();
 
-    if (!shouldProceed || !processedQuery) {
-      // An error occurred during @include processing (e.g., file not found).
-      // The error message is already logged by handleAtCommand.
-      throw new FatalInputError(
-        'Exiting due to an error processing the @ command.',
-      );
-    }
+      const { processedQuery, shouldProceed } = await handleAtCommand({
+        query: input,
+        config,
+        addItem: (_item, _timestamp) => 0,
+        onDebugMessage: () => {},
+        messageId: Date.now(),
+        signal: abortController.signal,
+      });
 
-    let currentMessages: Content[] = [
-      { role: 'user', parts: processedQuery as Part[] },
-    ];
-
-    let turnCount = 0;
-    while (true) {
-      turnCount++;
-      if (
-        config.getMaxSessionTurns() >= 0 &&
-        turnCount > config.getMaxSessionTurns()
-      ) {
-        throw new FatalTurnLimitedError(
-          'Reached max session turns for this session. Increase the number of turns by specifying maxSessionTurns in settings.json.',
+      if (!shouldProceed || !processedQuery) {
+        // An error occurred during @include processing (e.g., file not found).
+        // The error message is already logged by handleAtCommand.
+        throw new FatalInputError(
+          'Exiting due to an error processing the @ command.',
         );
       }
-      const toolCallRequests: ToolCallRequestInfo[] = [];
 
-      const responseStream = geminiClient.sendMessageStream(
-        currentMessages[0]?.parts || [],
-        abortController.signal,
-        prompt_id,
-      );
+      let currentMessages: Content[] = [
+        { role: 'user', parts: processedQuery as Part[] },
+      ];
 
-      for await (const event of responseStream) {
-        if (abortController.signal.aborted) {
-          console.error('Operation cancelled.');
+      let turnCount = 0;
+      while (true) {
+        turnCount++;
+        if (
+          config.getMaxSessionTurns() >= 0 &&
+          turnCount > config.getMaxSessionTurns()
+        ) {
+          throw new FatalTurnLimitedError(
+            'Reached max session turns for this session. Increase the number of turns by specifying maxSessionTurns in settings.json.',
+          );
+        }
+        const toolCallRequests: ToolCallRequestInfo[] = [];
+
+        const responseStream = geminiClient.sendMessageStream(
+          currentMessages[0]?.parts || [],
+          abortController.signal,
+          prompt_id,
+        );
+
+        for await (const event of responseStream) {
+          if (abortController.signal.aborted) {
+            console.error('Operation cancelled.');
+            return;
+          }
+
+          if (event.type === GeminiEventType.Content) {
+            process.stdout.write(event.value);
+          } else if (event.type === GeminiEventType.ToolCallRequest) {
+            toolCallRequests.push(event.value);
+          }
+        }
+
+        if (toolCallRequests.length > 0) {
+          const toolResponseParts: Part[] = [];
+          for (const requestInfo of toolCallRequests) {
+            const toolResponse = await executeToolCall(
+              config,
+              requestInfo,
+              abortController.signal,
+            );
+
+            if (toolResponse.error) {
+              console.error(
+                `Error executing tool ${requestInfo.name}: ${toolResponse.resultDisplay || toolResponse.error.message}`,
+              );
+            }
+
+            if (toolResponse.responseParts) {
+              toolResponseParts.push(...toolResponse.responseParts);
+            }
+          }
+          currentMessages = [{ role: 'user', parts: toolResponseParts }];
+        } else {
+          process.stdout.write('\n'); // Ensure a final newline
           return;
         }
-
-        if (event.type === GeminiEventType.Content) {
-          process.stdout.write(event.value);
-        } else if (event.type === GeminiEventType.ToolCallRequest) {
-          toolCallRequests.push(event.value);
-        }
       }
-
-      if (toolCallRequests.length > 0) {
-        const toolResponseParts: Part[] = [];
-        for (const requestInfo of toolCallRequests) {
-          const toolResponse = await executeToolCall(
-            config,
-            requestInfo,
-            abortController.signal,
-          );
-
-          if (toolResponse.error) {
-            console.error(
-              `Error executing tool ${requestInfo.name}: ${toolResponse.resultDisplay || toolResponse.error.message}`,
-            );
-          }
-
-          if (toolResponse.responseParts) {
-            toolResponseParts.push(...toolResponse.responseParts);
-          }
-        }
-        currentMessages = [{ role: 'user', parts: toolResponseParts }];
-      } else {
-        process.stdout.write('\n'); // Ensure a final newline
-        return;
+    } catch (error) {
+      console.error(
+        parseAndFormatApiError(
+          error,
+          config.getContentGeneratorConfig()?.authType,
+        ),
+      );
+      throw error;
+    } finally {
+      consolePatcher.cleanup();
+      if (isTelemetrySdkInitialized()) {
+        await shutdownTelemetry(config);
       }
     }
-  } catch (error) {
-    console.error(
-      parseAndFormatApiError(
-        error,
-        config.getContentGeneratorConfig()?.authType,
-      ),
-    );
-    throw error;
-  } finally {
-    consolePatcher.cleanup();
-    if (isTelemetrySdkInitialized()) {
-      await shutdownTelemetry(config);
-    }
-  }
+  });
 }

packages/cli/src/services/BuiltinCommandLoader.test.ts

@@ -15,7 +15,16 @@ vi.mock('../ui/commands/aboutCommand.js', async () => {
   };
 });
 
-vi.mock('../ui/commands/ideCommand.js', () => ({ ideCommand: vi.fn() }));
+vi.mock('../ui/commands/ideCommand.js', async () => {
+  const { CommandKind } = await import('../ui/commands/types.js');
+  return {
+    ideCommand: vi.fn().mockResolvedValue({
+      name: 'ide',
+      description: 'IDE command',
+      kind: CommandKind.BUILT_IN,
+    }),
+  };
+});
 vi.mock('../ui/commands/restoreCommand.js', () => ({
   restoreCommand: vi.fn(),
 }));
@@ -25,7 +34,6 @@ import { BuiltinCommandLoader } from './BuiltinCommandLoader.js';
 import type { Config } from '@google/gemini-cli-core';
 import { CommandKind } from '../ui/commands/types.js';
 
-import { ideCommand } from '../ui/commands/ideCommand.js';
 import { restoreCommand } from '../ui/commands/restoreCommand.js';
 
 vi.mock('../ui/commands/authCommand.js', () => ({ authCommand: {} }));
@@ -57,18 +65,12 @@ vi.mock('../ui/commands/mcpCommand.js', () => ({
 describe('BuiltinCommandLoader', () => {
   let mockConfig: Config;
 
-  const ideCommandMock = ideCommand as Mock;
   const restoreCommandMock = restoreCommand as Mock;
 
   beforeEach(() => {
     vi.clearAllMocks();
     mockConfig = { some: 'config' } as unknown as Config;
 
-    ideCommandMock.mockReturnValue({
-      name: 'ide',
-      description: 'IDE command',
-      kind: CommandKind.BUILT_IN,
-    });
     restoreCommandMock.mockReturnValue({
       name: 'restore',
       description: 'Restore command',
@@ -76,25 +78,23 @@ describe('BuiltinCommandLoader', () => {
     });
   });
 
-  it('should correctly pass the config object to command factory functions', async () => {
+  it('should correctly pass the config object to restore command factory', async () => {
     const loader = new BuiltinCommandLoader(mockConfig);
     await loader.loadCommands(new AbortController().signal);
 
-    expect(ideCommandMock).toHaveBeenCalledTimes(1);
-    expect(ideCommandMock).toHaveBeenCalledWith(mockConfig);
+    // ideCommand is now a constant, no longer needs config
     expect(restoreCommandMock).toHaveBeenCalledTimes(1);
     expect(restoreCommandMock).toHaveBeenCalledWith(mockConfig);
   });
 
   it('should filter out null command definitions returned by factories', async () => {
-    // Override the mock's behavior for this specific test.
-    ideCommandMock.mockReturnValue(null);
+    // ideCommand is now a constant SlashCommand
     const loader = new BuiltinCommandLoader(mockConfig);
     const commands = await loader.loadCommands(new AbortController().signal);
 
-    // The 'ide' command should be filtered out.
+    // The 'ide' command should be present.
     const ideCmd = commands.find((c) => c.name === 'ide');
-    expect(ideCmd).toBeUndefined();
+    expect(ideCmd).toBeDefined();
 
     // Other commands should still be present.
     const aboutCmd = commands.find((c) => c.name === 'about');
@@ -104,8 +104,7 @@ describe('BuiltinCommandLoader', () => {
   it('should handle a null config gracefully when calling factories', async () => {
     const loader = new BuiltinCommandLoader(null);
     await loader.loadCommands(new AbortController().signal);
-    expect(ideCommandMock).toHaveBeenCalledTimes(1);
-    expect(ideCommandMock).toHaveBeenCalledWith(null);
+    // ideCommand is now a constant, no longer needs config
     expect(restoreCommandMock).toHaveBeenCalledTimes(1);
     expect(restoreCommandMock).toHaveBeenCalledWith(null);
   });

packages/cli/src/services/BuiltinCommandLoader.ts

@@ -64,7 +64,7 @@ export class BuiltinCommandLoader implements ICommandLoader {
       editorCommand,
       extensionsCommand,
       helpCommand,
-      ideCommand(this.config),
+      await ideCommand(),
       initCommand,
       mcpCommand,
       memoryCommand,

packages/cli/src/services/FileCommandLoader.test.ts

@@ -224,6 +224,8 @@ describe('FileCommandLoader', () => {
     const mockConfig = {
       getProjectRoot: vi.fn(() => '/path/to/project'),
       getExtensions: vi.fn(() => []),
+      getFolderTrustFeature: vi.fn(() => false),
+      getFolderTrust: vi.fn(() => false),
     } as unknown as Config;
     const loader = new FileCommandLoader(mockConfig);
     const commands = await loader.loadCommands(signal);
@@ -267,6 +269,8 @@ describe('FileCommandLoader', () => {
     const mockConfig = {
       getProjectRoot: vi.fn(() => process.cwd()),
       getExtensions: vi.fn(() => []),
+      getFolderTrustFeature: vi.fn(() => false),
+      getFolderTrust: vi.fn(() => false),
     } as unknown as Config;
     const loader = new FileCommandLoader(mockConfig);
     const commands = await loader.loadCommands(signal);
@@ -556,6 +560,8 @@ describe('FileCommandLoader', () => {
             path: extensionDir,
           },
         ]),
+        getFolderTrustFeature: vi.fn(() => false),
+        getFolderTrust: vi.fn(() => false),
       } as unknown as Config;
       const loader = new FileCommandLoader(mockConfig);
       const commands = await loader.loadCommands(signal);
@@ -607,6 +613,8 @@ describe('FileCommandLoader', () => {
             path: extensionDir,
           },
         ]),
+        getFolderTrustFeature: vi.fn(() => false),
+        getFolderTrust: vi.fn(() => false),
       } as unknown as Config;
       const loader = new FileCommandLoader(mockConfig);
       const commands = await loader.loadCommands(signal);
@@ -714,6 +722,8 @@ describe('FileCommandLoader', () => {
             path: extensionDir2,
           },
         ]),
+        getFolderTrustFeature: vi.fn(() => false),
+        getFolderTrust: vi.fn(() => false),
       } as unknown as Config;
       const loader = new FileCommandLoader(mockConfig);
       const commands = await loader.loadCommands(signal);
@@ -750,6 +760,8 @@ describe('FileCommandLoader', () => {
             path: extensionDir,
           },
         ]),
+        getFolderTrustFeature: vi.fn(() => false),
+        getFolderTrust: vi.fn(() => false),
       } as unknown as Config;
       const loader = new FileCommandLoader(mockConfig);
       const commands = await loader.loadCommands(signal);
@@ -782,6 +794,8 @@ describe('FileCommandLoader', () => {
         getExtensions: vi.fn(() => [
           { name: 'a', version: '1.0.0', isActive: true, path: extensionDir },
         ]),
+        getFolderTrustFeature: vi.fn(() => false),
+        getFolderTrust: vi.fn(() => false),
       } as unknown as Config;
       const loader = new FileCommandLoader(mockConfig);
       const commands = await loader.loadCommands(signal);
@@ -1169,4 +1183,48 @@ describe('FileCommandLoader', () => {
       }
     });
   });
+
+  describe('with folder trust enabled', () => {
+    it('loads multiple commands', async () => {
+      const mockConfig = {
+        getProjectRoot: vi.fn(() => '/path/to/project'),
+        getExtensions: vi.fn(() => []),
+        getFolderTrustFeature: vi.fn(() => true),
+        getFolderTrust: vi.fn(() => true),
+      } as unknown as Config;
+      const userCommandsDir = Storage.getUserCommandsDir();
+      mock({
+        [userCommandsDir]: {
+          'test1.toml': 'prompt = "Prompt 1"',
+          'test2.toml': 'prompt = "Prompt 2"',
+        },
+      });
+
+      const loader = new FileCommandLoader(mockConfig);
+      const commands = await loader.loadCommands(signal);
+
+      expect(commands).toHaveLength(2);
+    });
+
+    it('does not load when folder is not trusted', async () => {
+      const mockConfig = {
+        getProjectRoot: vi.fn(() => '/path/to/project'),
+        getExtensions: vi.fn(() => []),
+        getFolderTrustFeature: vi.fn(() => true),
+        getFolderTrust: vi.fn(() => false),
+      } as unknown as Config;
+      const userCommandsDir = Storage.getUserCommandsDir();
+      mock({
+        [userCommandsDir]: {
+          'test1.toml': 'prompt = "Prompt 1"',
+          'test2.toml': 'prompt = "Prompt 2"',
+        },
+      });
+
+      const loader = new FileCommandLoader(mockConfig);
+      const commands = await loader.loadCommands(signal);
+
+      expect(commands).toHaveLength(0);
+    });
+  });
 });

packages/cli/src/services/FileCommandLoader.ts

@@ -63,8 +63,12 @@ const TomlCommandDefSchema = z.object({
  */
 export class FileCommandLoader implements ICommandLoader {
   private readonly projectRoot: string;
+  private readonly folderTrustEnabled: boolean;
+  private readonly folderTrust: boolean;
 
   constructor(private readonly config: Config | null) {
+    this.folderTrustEnabled = !!config?.getFolderTrustFeature();
+    this.folderTrust = !!config?.getFolderTrust();
     this.projectRoot = config?.getProjectRoot() || process.cwd();
   }
 
@@ -97,6 +101,10 @@ export class FileCommandLoader implements ICommandLoader {
           cwd: dirInfo.path,
         });
 
+        if (this.folderTrustEnabled && !this.folderTrust) {
+          return [];
+        }
+
         const commandPromises = files.map((file) =>
           this.parseAndAdaptFile(
             path.join(dirInfo.path, file),

packages/cli/src/ui/AppContainer.test.tsx

@@ -0,0 +1,559 @@
+/**
+ * @license
+ * Copyright 2025 Google LLC
+ * SPDX-License-Identifier: Apache-2.0
+ */
+
+import {
+  describe,
+  it,
+  expect,
+  vi,
+  beforeEach,
+  afterEach,
+  type Mock,
+} from 'vitest';
+import { render, cleanup } from 'ink-testing-library';
+import { AppContainer } from './AppContainer.js';
+import { type Config, makeFakeConfig } from '@google/gemini-cli-core';
+import type { LoadedSettings } from '../config/settings.js';
+import type { InitializationResult } from '../core/initializer.js';
+import { useQuotaAndFallback } from './hooks/useQuotaAndFallback.js';
+import { UIStateContext, type UIState } from './contexts/UIStateContext.js';
+import {
+  UIActionsContext,
+  type UIActions,
+} from './contexts/UIActionsContext.js';
+import { useContext } from 'react';
+
+// Helper component will read the context values provided by AppContainer
+// so we can assert against them in our tests.
+let capturedUIState: UIState;
+let capturedUIActions: UIActions;
+function TestContextConsumer() {
+  capturedUIState = useContext(UIStateContext)!;
+  capturedUIActions = useContext(UIActionsContext)!;
+  return null;
+}
+
+vi.mock('./App.js', () => ({
+  App: TestContextConsumer,
+}));
+
+vi.mock('./hooks/useQuotaAndFallback.js');
+vi.mock('./hooks/useHistoryManager.js');
+vi.mock('./hooks/useThemeCommand.js');
+vi.mock('./auth/useAuth.js');
+vi.mock('./hooks/useEditorSettings.js');
+vi.mock('./hooks/useSettingsCommand.js');
+vi.mock('./hooks/slashCommandProcessor.js');
+vi.mock('./hooks/useConsoleMessages.js');
+vi.mock('./hooks/useTerminalSize.js', () => ({
+  useTerminalSize: vi.fn(() => ({ columns: 80, rows: 24 })),
+}));
+vi.mock('./hooks/useGeminiStream.js');
+vi.mock('./hooks/vim.js');
+vi.mock('./hooks/useFocus.js');
+vi.mock('./hooks/useBracketedPaste.js');
+vi.mock('./hooks/useKeypress.js');
+vi.mock('./hooks/useLoadingIndicator.js');
+vi.mock('./hooks/useFolderTrust.js');
+vi.mock('./hooks/useMessageQueue.js');
+vi.mock('./hooks/useAutoAcceptIndicator.js');
+vi.mock('./hooks/useWorkspaceMigration.js');
+vi.mock('./hooks/useGitBranchName.js');
+vi.mock('./contexts/VimModeContext.js');
+vi.mock('./contexts/SessionContext.js');
+vi.mock('./components/shared/text-buffer.js');
+vi.mock('./hooks/useLogger.js');
+
+// Mock external utilities
+vi.mock('../utils/events.js');
+vi.mock('../utils/handleAutoUpdate.js');
+vi.mock('./utils/ConsolePatcher.js');
+vi.mock('../utils/cleanup.js');
+
+import { useHistory } from './hooks/useHistoryManager.js';
+import { useThemeCommand } from './hooks/useThemeCommand.js';
+import { useAuthCommand } from './auth/useAuth.js';
+import { useEditorSettings } from './hooks/useEditorSettings.js';
+import { useSettingsCommand } from './hooks/useSettingsCommand.js';
+import { useSlashCommandProcessor } from './hooks/slashCommandProcessor.js';
+import { useConsoleMessages } from './hooks/useConsoleMessages.js';
+import { useGeminiStream } from './hooks/useGeminiStream.js';
+import { useVim } from './hooks/vim.js';
+import { useFolderTrust } from './hooks/useFolderTrust.js';
+import { useMessageQueue } from './hooks/useMessageQueue.js';
+import { useAutoAcceptIndicator } from './hooks/useAutoAcceptIndicator.js';
+import { useWorkspaceMigration } from './hooks/useWorkspaceMigration.js';
+import { useGitBranchName } from './hooks/useGitBranchName.js';
+import { useVimMode } from './contexts/VimModeContext.js';
+import { useSessionStats } from './contexts/SessionContext.js';
+import { useTextBuffer } from './components/shared/text-buffer.js';
+import { useLogger } from './hooks/useLogger.js';
+import { useLoadingIndicator } from './hooks/useLoadingIndicator.js';
+
+describe('AppContainer State Management', () => {
+  let mockConfig: Config;
+  let mockSettings: LoadedSettings;
+  let mockInitResult: InitializationResult;
+
+  // Create typed mocks for all hooks
+  const mockedUseQuotaAndFallback = useQuotaAndFallback as Mock;
+  const mockedUseHistory = useHistory as Mock;
+  const mockedUseThemeCommand = useThemeCommand as Mock;
+  const mockedUseAuthCommand = useAuthCommand as Mock;
+  const mockedUseEditorSettings = useEditorSettings as Mock;
+  const mockedUseSettingsCommand = useSettingsCommand as Mock;
+  const mockedUseSlashCommandProcessor = useSlashCommandProcessor as Mock;
+  const mockedUseConsoleMessages = useConsoleMessages as Mock;
+  const mockedUseGeminiStream = useGeminiStream as Mock;
+  const mockedUseVim = useVim as Mock;
+  const mockedUseFolderTrust = useFolderTrust as Mock;
+  const mockedUseMessageQueue = useMessageQueue as Mock;
+  const mockedUseAutoAcceptIndicator = useAutoAcceptIndicator as Mock;
+  const mockedUseWorkspaceMigration = useWorkspaceMigration as Mock;
+  const mockedUseGitBranchName = useGitBranchName as Mock;
+  const mockedUseVimMode = useVimMode as Mock;
+  const mockedUseSessionStats = useSessionStats as Mock;
+  const mockedUseTextBuffer = useTextBuffer as Mock;
+  const mockedUseLogger = useLogger as Mock;
+  const mockedUseLoadingIndicator = useLoadingIndicator as Mock;
+
+  beforeEach(() => {
+    vi.clearAllMocks();
+
+    capturedUIState = null!;
+    capturedUIActions = null!;
+
+    // **Provide a default return value for EVERY mocked hook.**
+    mockedUseQuotaAndFallback.mockReturnValue({
+      proQuotaRequest: null,
+      handleProQuotaChoice: vi.fn(),
+    });
+    mockedUseHistory.mockReturnValue({
+      history: [],
+      addItem: vi.fn(),
+      updateItem: vi.fn(),
+      clearItems: vi.fn(),
+      loadHistory: vi.fn(),
+    });
+    mockedUseThemeCommand.mockReturnValue({
+      isThemeDialogOpen: false,
+      openThemeDialog: vi.fn(),
+      handleThemeSelect: vi.fn(),
+      handleThemeHighlight: vi.fn(),
+    });
+    mockedUseAuthCommand.mockReturnValue({
+      authState: 'authenticated',
+      setAuthState: vi.fn(),
+      authError: null,
+      onAuthError: vi.fn(),
+    });
+    mockedUseEditorSettings.mockReturnValue({
+      isEditorDialogOpen: false,
+      openEditorDialog: vi.fn(),
+      handleEditorSelect: vi.fn(),
+      exitEditorDialog: vi.fn(),
+    });
+    mockedUseSettingsCommand.mockReturnValue({
+      isSettingsDialogOpen: false,
+      openSettingsDialog: vi.fn(),
+      closeSettingsDialog: vi.fn(),
+    });
+    mockedUseSlashCommandProcessor.mockReturnValue({
+      handleSlashCommand: vi.fn(),
+      slashCommands: [],
+      pendingHistoryItems: [],
+      commandContext: {},
+      shellConfirmationRequest: null,
+      confirmationRequest: null,
+    });
+    mockedUseConsoleMessages.mockReturnValue({
+      consoleMessages: [],
+      handleNewMessage: vi.fn(),
+      clearConsoleMessages: vi.fn(),
+    });
+    mockedUseGeminiStream.mockReturnValue({
+      streamingState: 'idle',
+      submitQuery: vi.fn(),
+      initError: null,
+      pendingHistoryItems: [],
+      thought: null,
+      cancelOngoingRequest: vi.fn(),
+    });
+    mockedUseVim.mockReturnValue({ handleInput: vi.fn() });
+    mockedUseFolderTrust.mockReturnValue({
+      isFolderTrustDialogOpen: false,
+      handleFolderTrustSelect: vi.fn(),
+      isRestarting: false,
+    });
+    mockedUseMessageQueue.mockReturnValue({
+      messageQueue: [],
+      addMessage: vi.fn(),
+      clearQueue: vi.fn(),
+      getQueuedMessagesText: vi.fn().mockReturnValue(''),
+    });
+    mockedUseAutoAcceptIndicator.mockReturnValue(false);
+    mockedUseWorkspaceMigration.mockReturnValue({
+      showWorkspaceMigrationDialog: false,
+      workspaceExtensions: [],
+      onWorkspaceMigrationDialogOpen: vi.fn(),
+      onWorkspaceMigrationDialogClose: vi.fn(),
+    });
+    mockedUseGitBranchName.mockReturnValue('main');
+    mockedUseVimMode.mockReturnValue({
+      isVimEnabled: false,
+      toggleVimEnabled: vi.fn(),
+    });
+    mockedUseSessionStats.mockReturnValue({ stats: {} });
+    mockedUseTextBuffer.mockReturnValue({
+      text: '',
+      setText: vi.fn(),
+      // Add other properties if AppContainer uses them
+    });
+    mockedUseLogger.mockReturnValue({
+      getPreviousUserMessages: vi.fn().mockResolvedValue([]),
+    });
+    mockedUseLoadingIndicator.mockReturnValue({
+      elapsedTime: '0.0s',
+      currentLoadingPhrase: '',
+    });
+
+    // Mock Config
+    mockConfig = makeFakeConfig();
+
+    // Mock LoadedSettings
+    mockSettings = {
+      merged: {
+        hideBanner: false,
+        hideFooter: false,
+        hideTips: false,
+        showMemoryUsage: false,
+        theme: 'default',
+      },
+    } as unknown as LoadedSettings;
+
+    // Mock InitializationResult
+    mockInitResult = {
+      themeError: null,
+      authError: null,
+      shouldOpenAuthDialog: false,
+      geminiMdFileCount: 0,
+    } as InitializationResult;
+  });
+
+  afterEach(() => {
+    cleanup();
+  });
+
+  describe('Basic Rendering', () => {
+    it('renders without crashing with minimal props', () => {
+      expect(() => {
+        render(
+          <AppContainer
+            config={mockConfig}
+            settings={mockSettings}
+            version="1.0.0"
+            initializationResult={mockInitResult}
+          />,
+        );
+      }).not.toThrow();
+    });
+
+    it('renders with startup warnings', () => {
+      const startupWarnings = ['Warning 1', 'Warning 2'];
+
+      expect(() => {
+        render(
+          <AppContainer
+            config={mockConfig}
+            settings={mockSettings}
+            startupWarnings={startupWarnings}
+            version="1.0.0"
+            initializationResult={mockInitResult}
+          />,
+        );
+      }).not.toThrow();
+    });
+  });
+
+  describe('State Initialization', () => {
+    it('initializes with theme error from initialization result', () => {
+      const initResultWithError = {
+        ...mockInitResult,
+        themeError: 'Failed to load theme',
+      };
+
+      expect(() => {
+        render(
+          <AppContainer
+            config={mockConfig}
+            settings={mockSettings}
+            version="1.0.0"
+            initializationResult={initResultWithError}
+          />,
+        );
+      }).not.toThrow();
+    });
+
+    it('handles debug mode state', () => {
+      const debugConfig = makeFakeConfig();
+      vi.spyOn(debugConfig, 'getDebugMode').mockReturnValue(true);
+
+      expect(() => {
+        render(
+          <AppContainer
+            config={debugConfig}
+            settings={mockSettings}
+            version="1.0.0"
+            initializationResult={mockInitResult}
+          />,
+        );
+      }).not.toThrow();
+    });
+  });
+
+  describe('Context Providers', () => {
+    it('provides AppContext with correct values', () => {
+      const { unmount } = render(
+        <AppContainer
+          config={mockConfig}
+          settings={mockSettings}
+          version="2.0.0"
+          initializationResult={mockInitResult}
+        />,
+      );
+
+      // Should render and unmount cleanly
+      expect(() => unmount()).not.toThrow();
+    });
+
+    it('provides UIStateContext with state management', () => {
+      expect(() => {
+        render(
+          <AppContainer
+            config={mockConfig}
+            settings={mockSettings}
+            version="1.0.0"
+            initializationResult={mockInitResult}
+          />,
+        );
+      }).not.toThrow();
+    });
+
+    it('provides UIActionsContext with action handlers', () => {
+      expect(() => {
+        render(
+          <AppContainer
+            config={mockConfig}
+            settings={mockSettings}
+            version="1.0.0"
+            initializationResult={mockInitResult}
+          />,
+        );
+      }).not.toThrow();
+    });
+
+    it('provides ConfigContext with config object', () => {
+      expect(() => {
+        render(
+          <AppContainer
+            config={mockConfig}
+            settings={mockSettings}
+            version="1.0.0"
+            initializationResult={mockInitResult}
+          />,
+        );
+      }).not.toThrow();
+    });
+  });
+
+  describe('Settings Integration', () => {
+    it('handles settings with all display options disabled', () => {
+      const settingsAllHidden = {
+        merged: {
+          hideBanner: true,
+          hideFooter: true,
+          hideTips: true,
+          showMemoryUsage: false,
+        },
+      } as unknown as LoadedSettings;
+
+      expect(() => {
+        render(
+          <AppContainer
+            config={mockConfig}
+            settings={settingsAllHidden}
+            version="1.0.0"
+            initializationResult={mockInitResult}
+          />,
+        );
+      }).not.toThrow();
+    });
+
+    it('handles settings with memory usage enabled', () => {
+      const settingsWithMemory = {
+        merged: {
+          hideBanner: false,
+          hideFooter: false,
+          hideTips: false,
+          showMemoryUsage: true,
+        },
+      } as unknown as LoadedSettings;
+
+      expect(() => {
+        render(
+          <AppContainer
+            config={mockConfig}
+            settings={settingsWithMemory}
+            version="1.0.0"
+            initializationResult={mockInitResult}
+          />,
+        );
+      }).not.toThrow();
+    });
+  });
+
+  describe('Version Handling', () => {
+    it.each(['1.0.0', '2.1.3-beta', '3.0.0-nightly'])(
+      'handles version format: %s',
+      (version) => {
+        expect(() => {
+          render(
+            <AppContainer
+              config={mockConfig}
+              settings={mockSettings}
+              version={version}
+              initializationResult={mockInitResult}
+            />,
+          );
+        }).not.toThrow();
+      },
+    );
+  });
+
+  describe('Error Handling', () => {
+    it('handles config methods that might throw', () => {
+      const errorConfig = makeFakeConfig();
+      vi.spyOn(errorConfig, 'getModel').mockImplementation(() => {
+        throw new Error('Config error');
+      });
+
+      // Should still render without crashing - errors should be handled internally
+      expect(() => {
+        render(
+          <AppContainer
+            config={errorConfig}
+            settings={mockSettings}
+            version="1.0.0"
+            initializationResult={mockInitResult}
+          />,
+        );
+      }).not.toThrow();
+    });
+
+    it('handles undefined settings gracefully', () => {
+      const undefinedSettings = {
+        merged: {},
+      } as LoadedSettings;
+
+      expect(() => {
+        render(
+          <AppContainer
+            config={mockConfig}
+            settings={undefinedSettings}
+            version="1.0.0"
+            initializationResult={mockInitResult}
+          />,
+        );
+      }).not.toThrow();
+    });
+  });
+
+  describe('Provider Hierarchy', () => {
+    it('establishes correct provider nesting order', () => {
+      // This tests that all the context providers are properly nested
+      // and that the component tree can be built without circular dependencies
+      const { unmount } = render(
+        <AppContainer
+          config={mockConfig}
+          settings={mockSettings}
+          version="1.0.0"
+          initializationResult={mockInitResult}
+        />,
+      );
+
+      expect(() => unmount()).not.toThrow();
+    });
+  });
+
+  describe('Quota and Fallback Integration', () => {
+    it('passes a null proQuotaRequest to UIStateContext by default', () => {
+      // The default mock from beforeEach already sets proQuotaRequest to null
+      render(
+        <AppContainer
+          config={mockConfig}
+          settings={mockSettings}
+          version="1.0.0"
+          initializationResult={mockInitResult}
+        />,
+      );
+
+      // Assert that the context value is as expected
+      expect(capturedUIState.proQuotaRequest).toBeNull();
+    });
+
+    it('passes a valid proQuotaRequest to UIStateContext when provided by the hook', () => {
+      // Arrange: Create a mock request object that a UI dialog would receive
+      const mockRequest = {
+        failedModel: 'gemini-pro',
+        fallbackModel: 'gemini-flash',
+        resolve: vi.fn(),
+      };
+      mockedUseQuotaAndFallback.mockReturnValue({
+        proQuotaRequest: mockRequest,
+        handleProQuotaChoice: vi.fn(),
+      });
+
+      // Act: Render the container
+      render(
+        <AppContainer
+          config={mockConfig}
+          settings={mockSettings}
+          version="1.0.0"
+          initializationResult={mockInitResult}
+        />,
+      );
+
+      // Assert: The mock request is correctly passed through the context
+      expect(capturedUIState.proQuotaRequest).toEqual(mockRequest);
+    });
+
+    it('passes the handleProQuotaChoice function to UIActionsContext', () => {
+      // Arrange: Create a mock handler function
+      const mockHandler = vi.fn();
+      mockedUseQuotaAndFallback.mockReturnValue({
+        proQuotaRequest: null,
+        handleProQuotaChoice: mockHandler,
+      });
+
+      // Act: Render the container
+      render(
+        <AppContainer
+          config={mockConfig}
+          settings={mockSettings}
+          version="1.0.0"
+          initializationResult={mockInitResult}
+        />,
+      );
+
+      // Assert: The action in the context is the mock handler we provided
+      expect(capturedUIActions.handleProQuotaChoice).toBe(mockHandler);
+
+      // You can even verify that the plumbed function is callable
+      capturedUIActions.handleProQuotaChoice('auth');
+      expect(mockHandler).toHaveBeenCalledWith('auth');
+    });
+  });
+});