diff --git a/docs/architecture.md b/docs/architecture.md
deleted file mode 100644
index cf6ac8359d..0000000000
--- a/docs/architecture.md
+++ /dev/null
@@ -1,80 +0,0 @@
-# Gemini CLI Architecture Overview
-
-This document provides a high-level overview of the Gemini CLI's architecture.
-
-## Core components
-
-The Gemini CLI is primarily composed of two main packages, along with a suite of
-tools that can be used by the system in the course of handling command-line
-input:
-
-1.  **CLI package (`packages/cli`):**
-    - **Purpose:** This contains the user-facing portion of the Gemini CLI, such
-      as handling the initial user input, presenting the final output, and
-      managing the overall user experience.
-    - **Key functions contained in the package:**
-      - [Input processing](/docs/cli/commands)
-      - History management
-      - Display rendering
-      - [Theme and UI customization](/docs/cli/themes)
-      - [CLI configuration settings](/docs/get-started/configuration)
-
-2.  **Core package (`packages/core`):**
-    - **Purpose:** This acts as the backend for the Gemini CLI. It receives
-      requests sent from `packages/cli`, orchestrates interactions with the
-      Gemini API, and manages the execution of available tools.
-    - **Key functions contained in the package:**
-      - API client for communicating with the Google Gemini API
-      - Prompt construction and management
-      - Tool registration and execution logic
-      - State management for conversations or sessions
-      - Server-side configuration
-
-3.  **Tools (`packages/core/src/tools/`):**
-    - **Purpose:** These are individual modules that extend the capabilities of
-      the Gemini model, allowing it to interact with the local environment
-      (e.g., file system, shell commands, web fetching).
-    - **Interaction:** `packages/core` invokes these tools based on requests
-      from the Gemini model.
-
-## Interaction flow
-
-A typical interaction with the Gemini CLI follows this flow:
-
-1.  **User input:** The user types a prompt or command into the terminal, which
-    is managed by `packages/cli`.
-2.  **Request to core:** `packages/cli` sends the user's input to
-    `packages/core`.
-3.  **Request processed:** The core package:
-    - Constructs an appropriate prompt for the Gemini API, possibly including
-      conversation history and available tool definitions.
-    - Sends the prompt to the Gemini API.
-4.  **Gemini API response:** The Gemini API processes the prompt and returns a
-    response. This response might be a direct answer or a request to use one of
-    the available tools.
-5.  **Tool execution (if applicable):**
-    - When the Gemini API requests a tool, the core package prepares to execute
-      it.
-    - If the requested tool can modify the file system or execute shell
-      commands, the user is first given details of the tool and its arguments,
-      and the user must approve the execution.
-    - Read-only operations, such as reading files, might not require explicit
-      user confirmation to proceed.
-    - Once confirmed, or if confirmation is not required, the core package
-      executes the relevant action within the relevant tool, and the result is
-      sent back to the Gemini API by the core package.
-    - The Gemini API processes the tool result and generates a final response.
-6.  **Response to CLI:** The core package sends the final response back to the
-    CLI package.
-7.  **Display to user:** The CLI package formats and displays the response to
-    the user in the terminal.
-
-## Key design principles
-
-- **Modularity:** Separating the CLI (frontend) from the Core (backend) allows
-  for independent development and potential future extensions (e.g., different
-  frontends for the same backend).
-- **Extensibility:** The tool system is designed to be extensible, allowing new
-  capabilities to be added.
-- **User experience:** The CLI focuses on providing a rich and interactive
-  terminal experience.
diff --git a/docs/cli/plan-mode.md b/docs/cli/plan-mode.md
index 2cf01ae354..f09fefb035 100644
--- a/docs/cli/plan-mode.md
+++ b/docs/cli/plan-mode.md
@@ -180,7 +180,7 @@ Guide].
 [MCP tools]: /docs/tools/mcp-server.md
 [`activate_skill`]: /docs/cli/skills.md
 [experimental research sub-agents]: /docs/core/subagents.md
-[Policy Engine Guide]: /docs/core/policy-engine.md
+[Policy Engine Guide]: /docs/reference/policy-engine.md
 [`enter_plan_mode`]: /docs/tools/planning.md#1-enter_plan_mode-enterplanmode
 [`exit_plan_mode`]: /docs/tools/planning.md#2-exit_plan_mode-exitplanmode
 [`ask_user`]: /docs/tools/ask-user.md
diff --git a/docs/core/concepts.md b/docs/core/concepts.md
deleted file mode 100644
index 7a6e52c1b7..0000000000
--- a/docs/core/concepts.md
+++ /dev/null
@@ -1,137 +0,0 @@
-# Core concepts
-
-This guide explains the fundamental concepts and terminology used throughout the
-Gemini CLI ecosystem. Understanding these terms will help you make the most of
-the tool's capabilities.
-
-## Approval mode
-
-**Approval mode** determines the level of autonomy you grant to the agent when
-executing tools.
-
-- **Default:** The agent asks for confirmation before performing any potentially
-  impactful action (like writing files or running shell commands).
-- **Auto-edit:** File modifications are applied automatically, but shell
-  commands still require confirmation.
-- **YOLO (You Only Look Once):** The agent runs all tools without asking for
-  permission. High risk, high speed.
-
-## Checkpointing
-
-**Checkpointing** is a safety feature that automatically snapshots your
-project's file state before the agent performs any destructive action (like
-writing a file).
-
-- **Snapshots:** Stored in a hidden Git repository (separate from your project's
-  Git history).
-- **Restore:** Allows you to instantly revert changes if the agent makes a
-  mistake, using the `/restore` command.
-
-## Context
-
-**Context** refers to the information the agent has about your current task and
-environment. Gemini CLI provides context through several mechanisms:
-
-- **Conversation history:** The chat log of the current session.
-- **Project context (`GEMINI.md`):** Persistent instructions and rules defined
-  in your project's root or subdirectories.
-- **File content:** Files you explicitly reference (e.g., `@src/app.ts`) or that
-  the agent reads using tools.
-- **Environment:** Information about your operating system, shell, and working
-  directory.
-
-Effective context management is key to getting accurate and relevant responses.
-
-## Extension
-
-An **Extension** is a pluggable package that adds new capabilities to Gemini
-CLI. Extensions can bundle:
-
-- **Skills:** Specialized procedural knowledge.
-- **MCP Servers:** Connections to external tools and data.
-- **Commands:** Custom slash commands.
-
-## Headless mode
-
-**Headless mode** refers to running Gemini CLI without the interactive terminal
-UI (TUI). This is used for scripting, automation, and piping data into or out of
-the agent.
-
-- **Interactive:** `gemini` (starts the REPL).
-- **Headless:** `gemini "Fix this file"` (runs once and exits).
-
-## Hook
-
-A **Hook** is a script or function that intercepts specific lifecycle events in
-the CLI.
-
-- **Use cases:** Logging tool usage, validating user input, or modifying the
-  agent's system prompt dynamically.
-- **Lifecycle:** Hooks can run before or after the agent starts, before tools
-  are executed, or after the session ends.
-
-## Model Context Protocol (MCP)
-
-The **Model Context Protocol (MCP)** is an open standard that allows Gemini CLI
-to connect to external data sources and tools.
-
-- **MCP Server:** A lightweight application that exposes resources (data) and
-  tools (functions) to the CLI.
-- **Use case:** Connecting Gemini to a PostgreSQL database, a GitHub repository,
-  or a Slack workspace without building custom integration logic into the CLI
-  core.
-
-## Policy engine
-
-The **Policy Engine** is the security subsystem that enforces rules on tool
-execution. It evaluates every tool call against your configuration (e.g.,
-[Trusted folders](#trusted-folders), allowed commands) to decide whether to:
-
-- Allow the action immediately.
-- Require user confirmation.
-- Block the action entirely.
-
-## Sandboxing
-
-**Sandboxing** is an optional security mode that isolates the agent's execution
-environment. When enabled, the agent runs inside a secure container (e.g.,
-Docker), preventing it from accessing sensitive files or system resources
-outside of the designated workspace.
-
-## Session
-
-A **Session** is a single continuous interaction thread with the agent.
-
-- **State:** Sessions maintain conversation history and short-term memory.
-- **Persistence:** Sessions are automatically saved, allowing you to pause,
-  resume, or rewind them later.
-
-## Skill
-
-A **Skill** (or **Agent Skill**) is a package of specialized expertise that the
-agent can load on demand. Unlike general context, a skill provides specific
-procedural knowledge for a distinct task.
-
-- **Example:** A "Code Reviewer" skill might contain a checklist of security
-  vulnerabilities to look for and a specific format for reporting findings.
-- **Activation:** Skills are typically activated dynamically when the agent
-  recognizes a matching request.
-
-## Tool
-
-A **Tool** is a specific function or capability that the agent can execute.
-Tools allow the AI to interact with the outside world.
-
-- **Built-in tools:** Core capabilities like `read_file`, `run_shell_command`,
-  and `google_web_search`.
-- **MCP tools:** External tools provided by
-  [MCP servers](#model-context-protocol-mcp).
-
-When the agent uses a tool, it pauses generation, executes the code, and feeds
-the output back into its context window.
-
-## Trusted folders
-
-**Trusted folders** are specific directories you have explicitly authorized the
-agent to access without repeated confirmation prompts. This is a key component
-of the [Policy engine](#policy-engine) to balance security and usability.
diff --git a/docs/get-started/configuration-v1.md b/docs/get-started/configuration-v1.md
deleted file mode 100644
index cd1325b977..0000000000
--- a/docs/get-started/configuration-v1.md
+++ /dev/null
@@ -1,882 +0,0 @@
-# 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](../cli/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) [DEPRECATED]:
-  - **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`. **Deprecated**: Use the
-    [Policy Engine](../core/policy-engine.md) instead.
-  - **Example:** `"allowedTools": ["ShellTool(git status)"]`.
-
-- **`excludeTools`** (array of strings) [DEPRECATED]:
-  - **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.
-    **Deprecated**: Use the [Policy Engine](../core/policy-engine.md) instead.
-  - **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.
-
-- **`theme`** (string):
-  - **Description:** Sets the visual [theme](../cli/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](../cli/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](../cli/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
-    ```
-
-- **`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 and `.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.
-- **`HTTP_PROXY` / `HTTPS_PROXY`**:
-  - Specifies the proxy server to use for outgoing HTTP/HTTPS requests.
-  - Example: `export HTTPS_PROXY="http://proxy.example.com:8080"`
-- **`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.
-
-- **`--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](../cli/telemetry.md).
-- **`--telemetry-target`**:
-  - Sets the telemetry target. See [telemetry](../cli/telemetry.md) for more
-    information.
-- **`--telemetry-otlp-endpoint`**:
-  - Sets the OTLP endpoint for telemetry. See [telemetry](../cli/telemetry.md)
-    for more information.
-- **`--telemetry-otlp-protocol`**:
-  - Sets the OTLP protocol for telemetry (`grpc` or `http`). Defaults to `grpc`.
-    See [telemetry](../cli/telemetry.md) for more information.
-- **`--telemetry-log-prompts`**:
-  - Enables logging of prompts for telemetry. See
-    [telemetry](../cli/telemetry.md) for more information.
-- **`--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.
-- **`--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 and 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 and 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](../cli/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
-}
-```
diff --git a/docs/hooks/best-practices.md b/docs/hooks/best-practices.md
index 316aacbc29..763f4271c0 100644
--- a/docs/hooks/best-practices.md
+++ b/docs/hooks/best-practices.md
@@ -420,7 +420,7 @@ When you open a project with hooks defined in `.gemini/settings.json`:
 
 Hooks inherit the environment of the Gemini CLI process, which may include
 sensitive API keys. Gemini CLI provides a
-[redaction system](/docs/get-started/configuration#environment-variable-redaction)
+[redaction system](/docs/reference/configuration#environment-variable-redaction)
 that automatically filters variables matching sensitive patterns (e.g., `KEY`,
 `TOKEN`).
 
diff --git a/docs/index.md b/docs/index.md
index 9711d39e18..c571de8503 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -127,12 +127,9 @@ Settings and customization options for Gemini CLI.
 
 Deep technical documentation and API specifications.
 
-- **[Architecture overview](./architecture.md):** System design and components.
 - **[Command reference](./cli/commands.md):** Detailed slash command guide.
-- **[Configuration reference](./get-started/configuration.md):** Settings and
+- **[Configuration reference](./reference/configuration.md):** Settings and
   environment variables.
-- **[Core concepts](./core/concepts.md):** Fundamental terminology and
-  definitions.
 - **[Keyboard shortcuts](./cli/keyboard-shortcuts.md):** Productivity tips.
 - **[Policy engine](./core/policy-engine.md):** Fine-grained execution control.
 
diff --git a/docs/cli/commands.md b/docs/reference/commands.md
similarity index 100%
rename from docs/cli/commands.md
rename to docs/reference/commands.md
diff --git a/docs/get-started/configuration.md b/docs/reference/configuration.md
similarity index 99%
rename from docs/get-started/configuration.md
rename to docs/reference/configuration.md
index 5f6b89b9a2..686f2d3c64 100644
--- a/docs/get-started/configuration.md
+++ b/docs/reference/configuration.md
@@ -1,16 +1,5 @@
 # Gemini CLI configuration
 
-> **Note on configuration format, 9/17/25:** 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.
diff --git a/docs/cli/keyboard-shortcuts.md b/docs/reference/keyboard-shortcuts.md
similarity index 100%
rename from docs/cli/keyboard-shortcuts.md
rename to docs/reference/keyboard-shortcuts.md
diff --git a/docs/core/memport.md b/docs/reference/memport.md
similarity index 100%
rename from docs/core/memport.md
rename to docs/reference/memport.md
diff --git a/docs/core/policy-engine.md b/docs/reference/policy-engine.md
similarity index 100%
rename from docs/core/policy-engine.md
rename to docs/reference/policy-engine.md
diff --git a/docs/core/tools-api.md b/docs/reference/tools-api.md
similarity index 100%
rename from docs/core/tools-api.md
rename to docs/reference/tools-api.md
diff --git a/docs/faq.md b/docs/resources/faq.md
similarity index 100%
rename from docs/faq.md
rename to docs/resources/faq.md
diff --git a/docs/quota-and-pricing.md b/docs/resources/quota-and-pricing.md
similarity index 100%
rename from docs/quota-and-pricing.md
rename to docs/resources/quota-and-pricing.md
diff --git a/docs/tos-privacy.md b/docs/resources/tos-privacy.md
similarity index 96%
rename from docs/tos-privacy.md
rename to docs/resources/tos-privacy.md
index 0c7073e0fb..e653e59d1d 100644
--- a/docs/tos-privacy.md
+++ b/docs/resources/tos-privacy.md
@@ -10,8 +10,8 @@ and Privacy Notices applicable to those services apply to such access and use.
 Your Gemini CLI Usage Statistics are handled in accordance with Google's Privacy
 Policy.
 
-**Note:** See [quotas and pricing](/docs/quota-and-pricing.md) for the quota and
-pricing details that apply to your usage of the Gemini CLI.
+**Note:** See [quotas and pricing](/docs/resources/quota-and-pricing.md) for the
+quota and pricing details that apply to your usage of the Gemini CLI.
 
 ## Supported authentication methods
 
@@ -93,4 +93,4 @@ backend, these Terms of Service and Privacy Notice documents apply:
 
 You may opt-out from sending Gemini CLI Usage Statistics to Google by following
 the instructions available here:
-[Usage Statistics Configuration](https://github.com/google-gemini/gemini-cli/blob/main/docs/get-started/configuration.md#usage-statistics).
+[Usage Statistics Configuration](https://github.com/google-gemini/gemini-cli/blob/main/docs/reference/configuration.md#usage-statistics).
diff --git a/docs/troubleshooting.md b/docs/resources/troubleshooting.md
similarity index 100%
rename from docs/troubleshooting.md
rename to docs/resources/troubleshooting.md
diff --git a/docs/cli/uninstall.md b/docs/resources/uninstall.md
similarity index 100%
rename from docs/cli/uninstall.md
rename to docs/resources/uninstall.md
diff --git a/docs/sidebar.json b/docs/sidebar.json
index e59742274b..180dbb13d5 100644
--- a/docs/sidebar.json
+++ b/docs/sidebar.json
@@ -1,246 +1,315 @@
 [
   {
-    "label": "Get started",
-    "items": [
-      { "label": "Overview", "slug": "docs" },
-      { "label": "Quickstart", "slug": "docs/get-started" },
-      { "label": "Installation", "slug": "docs/get-started/installation" },
-      { "label": "Authentication", "slug": "docs/get-started/authentication" },
-      { "label": "Examples", "slug": "docs/get-started/examples" },
-      { "label": "CLI cheatsheet", "slug": "docs/cli/cli-reference" },
-      { "label": "Gemini 3 on Gemini CLI", "slug": "docs/get-started/gemini-3" }
-    ]
-  },
-  {
-    "label": "Use Gemini CLI",
+    "label": "docs_tab",
     "items": [
       {
-        "label": "File management",
-        "slug": "docs/cli/tutorials/file-management"
+        "label": "Get started",
+        "items": [
+          { "label": "Overview", "slug": "docs" },
+          { "label": "Quickstart", "slug": "docs/get-started" },
+          { "label": "Installation", "slug": "docs/get-started/installation" },
+          {
+            "label": "Authentication",
+            "slug": "docs/get-started/authentication"
+          },
+          { "label": "Examples", "slug": "docs/get-started/examples" },
+          { "label": "CLI cheatsheet", "slug": "docs/cli/cli-reference" },
+          {
+            "label": "Gemini 3 on Gemini CLI",
+            "slug": "docs/get-started/gemini-3"
+          }
+        ]
       },
       {
-        "label": "Manage context and memory",
-        "slug": "docs/cli/tutorials/memory-management"
+        "label": "Use Gemini CLI",
+        "items": [
+          {
+            "label": "File management",
+            "slug": "docs/cli/tutorials/file-management"
+          },
+          {
+            "label": "Manage context and memory",
+            "slug": "docs/cli/tutorials/memory-management"
+          },
+          {
+            "label": "Execute shell commands",
+            "slug": "docs/cli/tutorials/shell-commands"
+          },
+          {
+            "label": "Manage sessions and history",
+            "slug": "docs/cli/tutorials/session-management"
+          },
+          {
+            "label": "Plan tasks with todos",
+            "slug": "docs/cli/tutorials/task-planning"
+          },
+          {
+            "label": "Web search and fetch",
+            "slug": "docs/cli/tutorials/web-tools"
+          },
+          {
+            "label": "Get started with skills",
+            "slug": "docs/cli/tutorials/skills-getting-started"
+          },
+          {
+            "label": "Set up an MCP server",
+            "slug": "docs/cli/tutorials/mcp-setup"
+          },
+          { "label": "Automate tasks", "slug": "docs/cli/tutorials/automation" }
+        ]
       },
       {
-        "label": "Execute shell commands",
-        "slug": "docs/cli/tutorials/shell-commands"
-      },
-      {
-        "label": "Manage sessions and history",
-        "slug": "docs/cli/tutorials/session-management"
-      },
-      {
-        "label": "Plan tasks with todos",
-        "slug": "docs/cli/tutorials/task-planning"
-      },
-      {
-        "label": "Web search and fetch",
-        "slug": "docs/cli/tutorials/web-tools"
-      },
-      {
-        "label": "Get started with skills",
-        "slug": "docs/cli/tutorials/skills-getting-started"
-      },
-      {
-        "label": "Set up an MCP server",
-        "slug": "docs/cli/tutorials/mcp-setup"
-      },
-      { "label": "Automate tasks", "slug": "docs/cli/tutorials/automation" }
-    ]
-  },
-  {
-    "label": "Features",
-    "items": [
-      {
-        "label": "/about - About Gemini CLI",
-        "link": "/docs/cli/commands/#about"
-      },
-      {
-        "label": "/auth - Authentication",
-        "slug": "docs/get-started/authentication"
-      },
-      { "label": "/bug - Report a bug", "link": "/docs/cli/commands/#bug" },
-      { "label": "/chat - Chat history", "link": "/docs/cli/commands/#chat" },
-      { "label": "/clear - Clear screen", "link": "/docs/cli/commands/#clear" },
-      {
-        "label": "/compress - Compress context",
-        "link": "/docs/cli/commands/#compress"
-      },
-      { "label": "/copy - Copy output", "link": "/docs/cli/commands/#copy" },
-      {
-        "label": "/directory - Manage workspace",
-        "link": "/docs/cli/commands/#directory-or-dir"
-      },
-      {
-        "label": "/docs - Open documentation",
-        "link": "/docs/cli/commands/#docs"
-      },
-      {
-        "label": "/editor - Select editor",
-        "link": "/docs/cli/commands/#editor"
-      },
-      {
-        "label": "/extensions - Manage extensions",
-        "slug": "docs/extensions/index"
-      },
-      { "label": "/help - Show help", "link": "/docs/cli/commands/#help-or" },
-      { "label": "/hooks - Hooks", "slug": "docs/hooks" },
-      { "label": "/ide - IDE integration", "slug": "docs/ide-integration" },
-      {
-        "label": "/init - Initialize context",
-        "link": "/docs/cli/commands/#init"
-      },
-      { "label": "/mcp - MCP servers", "slug": "docs/tools/mcp-server" },
+        "label": "Features",
+        "items": [
+          {
+            "label": "/about - About Gemini CLI",
+            "link": "/docs/cli/commands/#about"
+          },
+          {
+            "label": "/auth - Authentication",
+            "slug": "docs/get-started/authentication"
+          },
+          { "label": "/bug - Report a bug", "link": "/docs/cli/commands/#bug" },
+          {
+            "label": "/chat - Chat history",
+            "link": "/docs/cli/commands/#chat"
+          },
+          {
+            "label": "/clear - Clear screen",
+            "link": "/docs/cli/commands/#clear"
+          },
+          {
+            "label": "/compress - Compress context",
+            "link": "/docs/cli/commands/#compress"
+          },
+          {
+            "label": "/copy - Copy output",
+            "link": "/docs/cli/commands/#copy"
+          },
+          {
+            "label": "/directory - Manage workspace",
+            "link": "/docs/cli/commands/#directory-or-dir"
+          },
+          {
+            "label": "/docs - Open documentation",
+            "link": "/docs/cli/commands/#docs"
+          },
+          {
+            "label": "/editor - Select editor",
+            "link": "/docs/cli/commands/#editor"
+          },
+          {
+            "label": "/extensions - Manage extensions",
+            "slug": "docs/extensions/index"
+          },
+          {
+            "label": "/help - Show help",
+            "link": "/docs/cli/commands/#help-or"
+          },
+          { "label": "/hooks - Hooks", "slug": "docs/hooks" },
+          { "label": "/ide - IDE integration", "slug": "docs/ide-integration" },
+          {
+            "label": "/init - Initialize context",
+            "link": "/docs/cli/commands/#init"
+          },
+          { "label": "/mcp - MCP servers", "slug": "docs/tools/mcp-server" },
 
-      {
-        "label": "/memory - Manage memory",
-        "link": "/docs/cli/commands/#memory"
-      },
-      { "label": "/model - Model selection", "slug": "docs/cli/model" },
-      {
-        "label": "/policies - Manage policies",
-        "link": "/docs/cli/commands/#policies"
-      },
-      {
-        "label": "/privacy - Privacy notice",
-        "link": "/docs/cli/commands/#privacy"
-      },
-      {
-        "label": "/quit - Exit CLI",
-        "link": "/docs/cli/commands/#quit-or-exit"
-      },
-      { "label": "/restore - Restore files", "slug": "docs/cli/checkpointing" },
-      {
-        "label": "/resume - Resume session",
+          {
+            "label": "/memory - Manage memory",
+            "link": "/docs/cli/commands/#memory"
+          },
+          { "label": "/model - Model selection", "slug": "docs/cli/model" },
+          {
+            "label": "/policies - Manage policies",
+            "link": "/docs/cli/commands/#policies"
+          },
+          {
+            "label": "/privacy - Privacy notice",
+            "link": "/docs/cli/commands/#privacy"
+          },
+          {
+            "label": "/quit - Exit CLI",
+            "link": "/docs/cli/commands/#quit-or-exit"
+          },
+          {
+            "label": "/restore - Restore files",
+            "slug": "docs/cli/checkpointing"
+          },
+          {
+            "label": "/resume - Resume session",
 
-        "link": "/docs/cli/commands/#resume"
-      },
-      { "label": "/rewind - Rewind", "slug": "docs/cli/rewind" },
-      { "label": "/settings - Settings", "slug": "docs/cli/settings" },
-      {
-        "label": "/setup-github - GitHub setup",
-        "link": "/docs/cli/commands/#setup-github"
-      },
-      {
-        "label": "/shells - Manage processes",
-        "link": "/docs/cli/commands/#shells-or-bashes"
-      },
-      { "label": "/skills - Agent skills", "slug": "docs/cli/skills" },
-      {
-        "label": "/stats - Session statistics",
-        "link": "/docs/cli/commands/#stats"
-      },
-      {
-        "label": "/terminal-setup - Terminal keybindings",
-        "link": "/docs/cli/commands/#terminal-setup"
-      },
-      { "label": "/theme - Themes", "slug": "docs/cli/themes" },
-      { "label": "/tools - List tools", "link": "/docs/cli/commands/#tools" },
-      { "label": "/vim - Vim mode", "link": "/docs/cli/commands/#vim" },
+            "link": "/docs/cli/commands/#resume"
+          },
+          { "label": "/rewind - Rewind", "slug": "docs/cli/rewind" },
+          { "label": "/settings - Settings", "slug": "docs/cli/settings" },
+          {
+            "label": "/setup-github - GitHub setup",
+            "link": "/docs/cli/commands/#setup-github"
+          },
+          {
+            "label": "/shells - Manage processes",
+            "link": "/docs/cli/commands/#shells-or-bashes"
+          },
+          { "label": "/skills - Agent skills", "slug": "docs/cli/skills" },
+          {
+            "label": "/stats - Session statistics",
+            "link": "/docs/cli/commands/#stats"
+          },
+          {
+            "label": "/terminal-setup - Terminal keybindings",
+            "link": "/docs/cli/commands/#terminal-setup"
+          },
+          { "label": "/theme - Themes", "slug": "docs/cli/themes" },
+          {
+            "label": "/tools - List tools",
+            "link": "/docs/cli/commands/#tools"
+          },
+          { "label": "/vim - Vim mode", "link": "/docs/cli/commands/#vim" },
 
-      {
-        "label": "Activate skill (tool)",
-        "slug": "docs/tools/activate-skill"
+          {
+            "label": "Activate skill (tool)",
+            "slug": "docs/tools/activate-skill"
+          },
+          { "label": "Ask user (tool)", "slug": "docs/tools/ask-user" },
+          { "label": "Checkpointing", "slug": "docs/cli/checkpointing" },
+          { "label": "File system (tool)", "slug": "docs/tools/file-system" },
+          { "label": "Headless mode", "slug": "docs/cli/headless" },
+          {
+            "label": "Internal documentation (tool)",
+            "slug": "docs/tools/internal-docs"
+          },
+          { "label": "Memory (tool)", "slug": "docs/tools/memory" },
+          { "label": "Model routing", "slug": "docs/cli/model-routing" },
+          { "label": "Plan mode (experimental)", "slug": "docs/cli/plan-mode" },
+          { "label": "Sandboxing", "slug": "docs/cli/sandbox" },
+          { "label": "Shell (tool)", "slug": "docs/tools/shell" },
+          { "label": "Telemetry", "slug": "docs/cli/telemetry" },
+          { "label": "Todo (tool)", "slug": "docs/tools/todos" },
+          { "label": "Token caching", "slug": "docs/cli/token-caching" },
+          { "label": "Web fetch (tool)", "slug": "docs/tools/web-fetch" },
+          { "label": "Web search (tool)", "slug": "docs/tools/web-search" }
+        ]
       },
-      { "label": "Ask user (tool)", "slug": "docs/tools/ask-user" },
-      { "label": "Checkpointing", "slug": "docs/cli/checkpointing" },
-      { "label": "File system (tool)", "slug": "docs/tools/file-system" },
-      { "label": "Headless mode", "slug": "docs/cli/headless" },
       {
-        "label": "Internal documentation (tool)",
-        "slug": "docs/tools/internal-docs"
+        "label": "Configuration",
+        "items": [
+          { "label": "Custom commands", "slug": "docs/cli/custom-commands" },
+          {
+            "label": "Enterprise configuration",
+            "slug": "docs/cli/enterprise"
+          },
+          {
+            "label": "Ignore files (.geminiignore)",
+            "slug": "docs/cli/gemini-ignore"
+          },
+          {
+            "label": "Model configuration",
+            "slug": "docs/cli/generation-settings"
+          },
+          {
+            "label": "Project context (GEMINI.md)",
+            "slug": "docs/cli/gemini-md"
+          },
+          { "label": "Settings", "slug": "docs/cli/settings" },
+          {
+            "label": "System prompt override",
+            "slug": "docs/cli/system-prompt"
+          },
+          { "label": "Themes", "slug": "docs/cli/themes" },
+          { "label": "Trusted folders", "slug": "docs/cli/trusted-folders" }
+        ]
       },
-      { "label": "Memory (tool)", "slug": "docs/tools/memory" },
-      { "label": "Model routing", "slug": "docs/cli/model-routing" },
-      { "label": "Plan mode (experimental)", "slug": "docs/cli/plan-mode" },
-      { "label": "Sandboxing", "slug": "docs/cli/sandbox" },
-      { "label": "Shell (tool)", "slug": "docs/tools/shell" },
-      { "label": "Telemetry", "slug": "docs/cli/telemetry" },
-      { "label": "Todo (tool)", "slug": "docs/tools/todos" },
-      { "label": "Token caching", "slug": "docs/cli/token-caching" },
-      { "label": "Web fetch (tool)", "slug": "docs/tools/web-fetch" },
-      { "label": "Web search (tool)", "slug": "docs/tools/web-search" }
+      {
+        "label": "Extensions",
+        "items": [
+          { "label": "Introduction", "slug": "docs/extensions" },
+          {
+            "label": "Writing extensions",
+            "slug": "docs/extensions/writing-extensions"
+          },
+          { "label": "Reference", "slug": "docs/extensions/reference" },
+          {
+            "label": "Best practices",
+            "slug": "docs/extensions/best-practices"
+          },
+          { "label": "Releasing", "slug": "docs/extensions/releasing" }
+        ]
+      },
+      {
+        "label": "Development",
+        "items": [
+          { "label": "Contribution guide", "slug": "docs/contributing" },
+          { "label": "Integration testing", "slug": "docs/integration-tests" },
+          {
+            "label": "Issue and PR automation",
+            "slug": "docs/issue-and-pr-automation"
+          },
+          { "label": "Local development", "slug": "docs/local-development" },
+          { "label": "NPM package structure", "slug": "docs/npm" }
+        ]
+      }
     ]
   },
   {
-    "label": "Configuration",
+    "label": "reference_tab",
     "items": [
-      { "label": "Custom commands", "slug": "docs/cli/custom-commands" },
-      { "label": "Enterprise configuration", "slug": "docs/cli/enterprise" },
       {
-        "label": "Ignore files (.geminiignore)",
-        "slug": "docs/cli/gemini-ignore"
-      },
-      {
-        "label": "Model configuration",
-        "slug": "docs/cli/generation-settings"
-      },
-      { "label": "Project context (GEMINI.md)", "slug": "docs/cli/gemini-md" },
-      { "label": "Settings", "slug": "docs/cli/settings" },
-      { "label": "System prompt override", "slug": "docs/cli/system-prompt" },
-      { "label": "Themes", "slug": "docs/cli/themes" },
-      { "label": "Trusted folders", "slug": "docs/cli/trusted-folders" }
+        "label": "Reference",
+        "items": [
+          { "label": "Command reference", "slug": "docs/reference/commands" },
+          {
+            "label": "Configuration reference",
+            "slug": "docs/reference/configuration"
+          },
+          {
+            "label": "Keyboard shortcuts",
+            "slug": "docs/reference/keyboard-shortcuts"
+          },
+          {
+            "label": "Memory import processor",
+            "slug": "docs/reference/memport"
+          },
+          { "label": "Policy engine", "slug": "docs/reference/policy-engine" },
+          { "label": "Tools API", "slug": "docs/reference/tools-api" }
+        ]
+      }
     ]
   },
   {
-    "label": "Extensions",
+    "label": "resources_tab",
     "items": [
-      { "label": "Introduction", "slug": "docs/extensions" },
       {
-        "label": "Writing extensions",
-        "slug": "docs/extensions/writing-extensions"
-      },
-      { "label": "Reference", "slug": "docs/extensions/reference" },
-      { "label": "Best practices", "slug": "docs/extensions/best-practices" },
-      { "label": "Releasing", "slug": "docs/extensions/releasing" }
+        "label": "Resources",
+        "items": [
+          {
+            "label": "Quota and pricing",
+            "slug": "docs/resources/quota-and-pricing"
+          },
+          {
+            "label": "Terms and privacy",
+            "slug": "docs/resources/tos-privacy"
+          },
+          { "label": "FAQ", "slug": "docs/resources/faq" },
+          {
+            "label": "Troubleshooting",
+            "slug": "docs/resources/troubleshooting"
+          },
+          { "label": "Uninstall", "slug": "docs/resources/uninstall" }
+        ]
+      }
     ]
   },
   {
-    "label": "Reference",
+    "label": "changelog_tab",
     "items": [
-      { "label": "Architecture", "slug": "docs/architecture" },
-      { "label": "Command reference", "slug": "docs/cli/commands" },
       {
-        "label": "Configuration reference",
-        "slug": "docs/get-started/configuration"
-      },
-      { "label": "Core concepts", "slug": "docs/core/concepts" },
-      { "label": "Keyboard shortcuts", "slug": "docs/cli/keyboard-shortcuts" },
-      { "label": "Memory import processor", "slug": "docs/core/memport" },
-      { "label": "Policy engine", "slug": "docs/core/policy-engine" },
-      { "label": "Tools API", "slug": "docs/core/tools-api" }
-    ]
-  },
-  {
-    "label": "Resources",
-    "items": [
-      { "label": "FAQ", "slug": "docs/faq" },
-      { "label": "Quota and pricing", "slug": "docs/quota-and-pricing" },
-      { "label": "Terms and privacy", "slug": "docs/tos-privacy" },
-      { "label": "Troubleshooting", "slug": "docs/troubleshooting" },
-      { "label": "Uninstall", "slug": "docs/cli/uninstall" }
-    ]
-  },
-  {
-    "label": "Development",
-    "items": [
-      { "label": "Contribution guide", "slug": "docs/contributing" },
-      { "label": "Integration testing", "slug": "docs/integration-tests" },
-      {
-        "label": "Issue and PR automation",
-        "slug": "docs/issue-and-pr-automation"
-      },
-      { "label": "Local development", "slug": "docs/local-development" },
-      { "label": "NPM package structure", "slug": "docs/npm" }
-    ]
-  },
-  {
-    "label": "Releases",
-    "items": [
-      { "label": "Release notes", "slug": "docs/changelogs/" },
-      { "label": "Stable release", "slug": "docs/changelogs/latest" },
-      { "label": "Preview release", "slug": "docs/changelogs/preview" }
+        "label": "Changelog",
+        "items": [
+          { "label": "Release notes", "slug": "docs/changelogs/" },
+          { "label": "Stable release", "slug": "docs/changelogs/latest" },
+          { "label": "Preview release", "slug": "docs/changelogs/preview" }
+        ]
+      }
     ]
   }
 ]
diff --git a/scripts/generate-settings-doc.ts b/scripts/generate-settings-doc.ts
index 32d9d47c0b..1d27eb962a 100644
--- a/scripts/generate-settings-doc.ts
+++ b/scripts/generate-settings-doc.ts
@@ -47,7 +47,7 @@ export async function main(argv = process.argv.slice(2)) {
     path.dirname(fileURLToPath(import.meta.url)),
     '..',
   );
-  const docPath = path.join(repoRoot, 'docs/get-started/configuration.md');
+  const docPath = path.join(repoRoot, 'docs/reference/configuration.md');
   const cliSettingsDocPath = path.join(repoRoot, 'docs/cli/settings.md');
 
   const { getSettingsSchema } = await loadSettingsSchemaModule();