diff --git a/docs/cli/commands.md b/docs/cli/commands.md
index 3508f6e1c3..3b94bd7495 100644
--- a/docs/cli/commands.md
+++ b/docs/cli/commands.md
@@ -21,7 +21,7 @@ Slash commands provide meta-level control over the CLI itself.
         - Linux/macOS: `~/.gemini/tmp/<project_hash>/`
         - Windows: `C:\Users\<YourUsername>\.gemini\tmp\<project_hash>\`
         - When you run `/chat list`, the CLI only scans these specific directories to find available checkpoints.
-        - **Note:** These checkpoints are for manually saving and resuming conversation states. For automatic checkpoints created before file modifications, see the [Checkpointing documentation](./checkpointing.md).
+        - **Note:** These checkpoints are for manually saving and resuming conversation states. For automatic checkpoints created before file modifications, see the [Checkpointing documentation](../cli/checkpointing.md).
     - **`resume`**
       - **Description:** Resumes a conversation from a previous save.
       - **Usage:** `/chat resume <tag>`
@@ -94,7 +94,7 @@ Slash commands provide meta-level control over the CLI itself.
 - **`/restore`**
   - **Description:** Restores the project files to the state they were in just before a tool was executed. This is particularly useful for undoing file edits made by a tool. If run without a tool call ID, it will list available checkpoints to restore from.
   - **Usage:** `/restore [tool_call_id]`
-  - **Note:** Only available if the CLI is invoked with the `--checkpointing` option or configured via [settings](../get-started/configuration.md). See [Checkpointing documentation](../checkpointing.md) for more details.
+  - **Note:** Only available if the CLI is invoked with the `--checkpointing` option or configured via [settings](../get-started/configuration.md). See [Checkpointing documentation](../cli/checkpointing.md) for more details.
 
 - **`/settings`**
   - **Description:** Open the settings editor to view and modify Gemini CLI settings.
diff --git a/docs/get-started/configuration-v1.md b/docs/get-started/configuration-v1.md
index 02fabbdb5e..c0d573f116 100644
--- a/docs/get-started/configuration-v1.md
+++ b/docs/get-started/configuration-v1.md
@@ -131,7 +131,7 @@ If you are experiencing performance issues with file searching (e.g., with `@` c
   - **Example:** `"autoAccept": true`
 
 - **`theme`** (string):
-  - **Description:** Sets the visual [theme](./themes.md) for Gemini CLI.
+  - **Description:** Sets the visual [theme](../cli/themes.md) for Gemini CLI.
   - **Default:** `"Default"`
   - **Example:** `"theme": "GitHub"`
 
@@ -216,7 +216,7 @@ If you are experiencing performance issues with file searching (e.g., with `@` c
     ```
 
 - **`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.
+  - **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.
@@ -227,7 +227,7 @@ If you are experiencing performance issues with file searching (e.g., with `@` c
   - **Example:** `"preferredEditor": "vscode"`
 
 - **`telemetry`** (object)
-  - **Description:** Configures logging and metrics collection for Gemini CLI. For more information, see [Telemetry](../telemetry.md).
+  - **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.
@@ -497,17 +497,17 @@ Arguments passed directly when running the CLI can override other configurations
   - 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).
+  - Enables [telemetry](../cli/telemetry.md).
 - **`--telemetry-target`**:
-  - Sets the telemetry target. See [telemetry](../telemetry.md) for more information.
+  - Sets the telemetry target. See [telemetry](../cli/telemetry.md) for more information.
 - **`--telemetry-otlp-endpoint`**:
-  - Sets the OTLP endpoint for telemetry. See [telemetry](../telemetry.md) for more information.
+  - 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](../telemetry.md) for more information.
+  - 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](../telemetry.md) for more information.
+  - Enables logging of prompts for telemetry. See [telemetry](../cli/telemetry.md) for more information.
 - **`--checkpointing`**:
-  - Enables [checkpointing](../checkpointing.md).
+  - Enables [checkpointing](../cli/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.
diff --git a/docs/get-started/configuration.md b/docs/get-started/configuration.md
index bb8dcd534d..340a1bea28 100644
--- a/docs/get-started/configuration.md
+++ b/docs/get-started/configuration.md
@@ -302,7 +302,7 @@ Configures connections to one or more Model-Context Protocol (MCP) servers for d
 
 #### `telemetry`
 
-Configures logging and metrics collection for Gemini CLI. For more information, see [Telemetry](../telemetry.md).
+Configures logging and metrics collection for Gemini CLI. For more information, see [Telemetry](../cli/telemetry.md).
 
 - **Properties:**
   - **`enabled`** (boolean): Whether or not telemetry is enabled.
@@ -514,17 +514,17 @@ Arguments passed directly when running the CLI can override other configurations
   - 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).
+  - Enables [telemetry](../cli/telemetry.md).
 - **`--telemetry-target`**:
-  - Sets the telemetry target. See [telemetry](../telemetry.md) for more information.
+  - Sets the telemetry target. See [telemetry](../cli/telemetry.md) for more information.
 - **`--telemetry-otlp-endpoint`**:
-  - Sets the OTLP endpoint for telemetry. See [telemetry](../telemetry.md) for more information.
+  - 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](../telemetry.md) for more information.
+  - 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](../telemetry.md) for more information.
+  - Enables logging of prompts for telemetry. See [telemetry](../cli/telemetry.md) for more information.
 - **`--checkpointing`**:
-  - Enables [checkpointing](../checkpointing.md).
+  - Enables [checkpointing](../cli/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.
diff --git a/docs/getting-started-extensions.md b/docs/getting-started-extensions.md
index d84b116131..2622141723 100644
--- a/docs/getting-started-extensions.md
+++ b/docs/getting-started-extensions.md
@@ -198,7 +198,7 @@ Restart the CLI again. The model will now have the context from your `GEMINI.md`
 
 Once you are happy with your extension, you can share it with others. The two primary ways of releasing extensions are via a Git repository or through GitHub Releases. Using a public Git repository is the simplest method.
 
-For detailed instructions on both methods, please refer to the [Extension Releasing Guide](extension-releasing.md).
+For detailed instructions on both methods, please refer to the [Extension Releasing Guide](./extensions/extension-releasing.md).
 
 ## Conclusion