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2 changes: 1 addition & 1 deletion CONTRIBUTING.md
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Expand Up @@ -546,7 +546,7 @@ Before submitting your documentation pull request, please:

If you have questions about contributing documentation:

- Check our [FAQ](/docs/faq.md).
- Check our [FAQ](/docs/resources/faq.md).
- Review existing documentation for examples.
- Open [an issue](https://github.com/google-gemini/gemini-cli/issues) to discuss
your proposed changes.
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3 changes: 2 additions & 1 deletion docs/changelogs/index.md
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Expand Up @@ -295,7 +295,8 @@ on GitHub.
- **Experimental permission improvements:** We are now experimenting with a new
policy engine in Gemini CLI. This allows users and administrators to create
fine-grained policy for tool calls. Currently behind a flag. See
[policy engine documentation](../core/policy-engine.md) for more information.
[policy engine documentation](../reference/policy-engine.md) for more
information.
- Blog:
[https://allen.hutchison.org/2025/11/26/the-guardrails-of-autonomy/](https://allen.hutchison.org/2025/11/26/the-guardrails-of-autonomy/)
- **Gemini 3 support for paid:** Gemini 3 support has been rolled out to all API
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46 changes: 23 additions & 23 deletions docs/cli/cli-reference.md
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Expand Up @@ -26,29 +26,29 @@ and parameters.

## CLI Options

| Option | Alias | Type | Default | Description |
| -------------------------------- | ----- | ------- | --------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| `--debug` | `-d` | boolean | `false` | Run in debug mode with verbose logging |
| `--version` | `-v` | - | - | Show CLI version number and exit |
| `--help` | `-h` | - | - | Show help information |
| `--model` | `-m` | string | `auto` | Model to use. See [Model Selection](#model-selection) for available values. |
| `--prompt` | `-p` | string | - | Prompt text. Appended to stdin input if provided. **Deprecated:** Use positional arguments instead. |
| `--prompt-interactive` | `-i` | string | - | Execute prompt and continue in interactive mode |
| `--sandbox` | `-s` | boolean | `false` | Run in a sandboxed environment for safer execution |
| `--approval-mode` | - | string | `default` | Approval mode for tool execution. Choices: `default`, `auto_edit`, `yolo` |
| `--yolo` | `-y` | boolean | `false` | **Deprecated.** Auto-approve all actions. Use `--approval-mode=yolo` instead. |
| `--experimental-acp` | - | boolean | - | Start in ACP (Agent Code Pilot) mode. **Experimental feature.** |
| `--experimental-zed-integration` | - | boolean | - | Run in Zed editor integration mode. **Experimental feature.** |
| `--allowed-mcp-server-names` | - | array | - | Allowed MCP server names (comma-separated or multiple flags) |
| `--allowed-tools` | - | array | - | **Deprecated.** Use the [Policy Engine](../core/policy-engine.md) instead. Tools that are allowed to run without confirmation (comma-separated or multiple flags) |
| `--extensions` | `-e` | array | - | List of extensions to use. If not provided, all extensions are enabled (comma-separated or multiple flags) |
| `--list-extensions` | `-l` | boolean | - | List all available extensions and exit |
| `--resume` | `-r` | string | - | Resume a previous session. Use `"latest"` for most recent or index number (e.g. `--resume 5`) |
| `--list-sessions` | - | boolean | - | List available sessions for the current project and exit |
| `--delete-session` | - | string | - | Delete a session by index number (use `--list-sessions` to see available sessions) |
| `--include-directories` | - | array | - | Additional directories to include in the workspace (comma-separated or multiple flags) |
| `--screen-reader` | - | boolean | - | Enable screen reader mode for accessibility |
| `--output-format` | `-o` | string | `text` | The format of the CLI output. Choices: `text`, `json`, `stream-json` |
| Option | Alias | Type | Default | Description |
| -------------------------------- | ----- | ------- | --------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| `--debug` | `-d` | boolean | `false` | Run in debug mode with verbose logging |
| `--version` | `-v` | - | - | Show CLI version number and exit |
| `--help` | `-h` | - | - | Show help information |
| `--model` | `-m` | string | `auto` | Model to use. See [Model Selection](#model-selection) for available values. |
| `--prompt` | `-p` | string | - | Prompt text. Appended to stdin input if provided. **Deprecated:** Use positional arguments instead. |
| `--prompt-interactive` | `-i` | string | - | Execute prompt and continue in interactive mode |
| `--sandbox` | `-s` | boolean | `false` | Run in a sandboxed environment for safer execution |
| `--approval-mode` | - | string | `default` | Approval mode for tool execution. Choices: `default`, `auto_edit`, `yolo` |
| `--yolo` | `-y` | boolean | `false` | **Deprecated.** Auto-approve all actions. Use `--approval-mode=yolo` instead. |
| `--experimental-acp` | - | boolean | - | Start in ACP (Agent Code Pilot) mode. **Experimental feature.** |
| `--experimental-zed-integration` | - | boolean | - | Run in Zed editor integration mode. **Experimental feature.** |
| `--allowed-mcp-server-names` | - | array | - | Allowed MCP server names (comma-separated or multiple flags) |
| `--allowed-tools` | - | array | - | **Deprecated.** Use the [Policy Engine](../reference/policy-engine.md) instead. Tools that are allowed to run without confirmation (comma-separated or multiple flags) |
| `--extensions` | `-e` | array | - | List of extensions to use. If not provided, all extensions are enabled (comma-separated or multiple flags) |
| `--list-extensions` | `-l` | boolean | - | List all available extensions and exit |
| `--resume` | `-r` | string | - | Resume a previous session. Use `"latest"` for most recent or index number (e.g. `--resume 5`) |
| `--list-sessions` | - | boolean | - | List available sessions for the current project and exit |
| `--delete-session` | - | string | - | Delete a session by index number (use `--list-sessions` to see available sessions) |
| `--include-directories` | - | array | - | Additional directories to include in the workspace (comma-separated or multiple flags) |
| `--screen-reader` | - | boolean | - | Enable screen reader mode for accessibility |
| `--output-format` | `-o` | string | `text` | The format of the CLI output. Choices: `text`, `json`, `stream-json` |

## Model selection

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14 changes: 7 additions & 7 deletions docs/cli/enterprise.md
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Expand Up @@ -20,7 +20,7 @@ The most powerful tools for enterprise administration are the system-wide
settings files. These files allow you to define a baseline configuration
(`system-defaults.json`) and a set of overrides (`settings.json`) that apply to
all users on a machine. For a complete overview of configuration options, see
the [Configuration documentation](../get-started/configuration.md).
the [Configuration documentation](../reference/configuration.md).

Settings are merged from four files. The precedence order for single-value
settings (like `theme`) is:
Expand Down Expand Up @@ -224,8 +224,8 @@ gemini

You can significantly enhance security by controlling which tools the Gemini
model can use. This is achieved through the `tools.core` setting and the
[Policy Engine](../core/policy-engine.md). For a list of available tools, see
the [Tools documentation](../tools/index.md).
[Policy Engine](../reference/policy-engine.md). For a list of available tools,
see the [Tools documentation](../tools/index.md).

### Allowlisting with `coreTools`

Expand All @@ -245,8 +245,8 @@ on the approved list.

### Blocklisting with `excludeTools` (Deprecated)

> **Deprecated:** Use the [Policy Engine](../core/policy-engine.md) for more
> robust control.
> **Deprecated:** Use the [Policy Engine](../reference/policy-engine.md) for
> more robust control.

Alternatively, you can add specific tools that are considered dangerous in your
environment to a blocklist.
Expand Down Expand Up @@ -289,8 +289,8 @@ unintended tool execution.
## Managing custom tools (MCP servers)

If your organization uses custom tools via
[Model-Context Protocol (MCP) servers](../core/tools-api.md), it is crucial to
understand how server configurations are managed to apply security policies
[Model-Context Protocol (MCP) servers](../reference/tools-api.md), it is crucial
to understand how server configurations are managed to apply security policies
effectively.

### How MCP server configurations are merged
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2 changes: 1 addition & 1 deletion docs/cli/gemini-md.md
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Expand Up @@ -88,7 +88,7 @@ More content here.
@../shared/style-guide.md
```

For more details, see the [Memory Import Processor](../core/memport.md)
For more details, see the [Memory Import Processor](../reference/memport.md)
documentation.

## Customize the context file name
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2 changes: 1 addition & 1 deletion docs/cli/model.md
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Expand Up @@ -39,7 +39,7 @@ To enable Gemini 3 Pro and Gemini 3 Flash (if available), enable

You can also use the `--model` flag to specify a particular Gemini model on
startup. For more details, refer to the
[configuration documentation](../get-started/configuration.md).
[configuration documentation](../reference/configuration.md).

Changes to these settings will be applied to all subsequent interactions with
Gemini CLI.
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2 changes: 1 addition & 1 deletion docs/cli/plan-mode.md
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Expand Up @@ -225,7 +225,7 @@ 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
6 changes: 3 additions & 3 deletions docs/cli/sandbox.md
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Expand Up @@ -167,6 +167,6 @@ gemini -s -p "run shell command: mount | grep workspace"

## Related documentation

- [Configuration](../get-started/configuration.md): Full configuration options.
- [Commands](./commands.md): Available commands.
- [Troubleshooting](../troubleshooting.md): General troubleshooting.
- [Configuration](../reference/configuration.md): Full configuration options.
- [Commands](../reference/commands.md): Available commands.
- [Troubleshooting](../resources/troubleshooting.md): General troubleshooting.
2 changes: 1 addition & 1 deletion docs/cli/telemetry.md
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Expand Up @@ -93,7 +93,7 @@ Environment variables can be used to override the settings in the file.
`true` or `1` will enable the feature. Any other value will disable it.

For detailed information about all configuration options, see the
[Configuration guide](../get-started/configuration.md).
[Configuration guide](../reference/configuration.md).

## Google Cloud telemetry

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6 changes: 3 additions & 3 deletions docs/cli/themes.md
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Expand Up @@ -41,8 +41,8 @@ can change the theme using the `/theme` command.
### Theme persistence

Selected themes are saved in Gemini CLI's
[configuration](../get-started/configuration.md) so your preference is
remembered across sessions.
[configuration](../reference/configuration.md) so your preference is remembered
across sessions.

---

Expand Down Expand Up @@ -194,7 +194,7 @@ untrusted sources.
- 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](../get-started/configuration.md) as other
same [configuration precedence](../reference/configuration.md) as other
settings.

### Themes from extensions
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4 changes: 2 additions & 2 deletions docs/cli/tutorials/memory-management.md
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Expand Up @@ -121,6 +121,6 @@ immediately. Force a reload with:

- Learn about [Session management](session-management.md) to see how short-term
history works.
- Explore the [Command reference](../../cli/commands.md) for more `/memory`
options.
- Explore the [Command reference](../../reference/commands.md) for more
`/memory` options.
- Read the technical spec for [Project context](../../cli/gemini-md.md).
2 changes: 1 addition & 1 deletion docs/cli/tutorials/session-management.md
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Expand Up @@ -101,5 +101,5 @@ This creates a new branch of history without losing your original work.
- Learn about [Checkpointing](../../cli/checkpointing.md) to understand the
underlying safety mechanism.
- Explore [Task planning](task-planning.md) to keep complex sessions organized.
- See the [Command reference](../../cli/commands.md) for all `/chat` and
- See the [Command reference](../../reference/commands.md) for all `/chat` and
`/resume` options.
14 changes: 7 additions & 7 deletions docs/core/index.md
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Expand Up @@ -9,11 +9,11 @@ requests sent from `packages/cli`. For a general overview of Gemini CLI, see the

- **[Sub-agents (experimental)](./subagents.md):** Learn how to create and use
specialized sub-agents for complex tasks.
- **[Core tools API](./tools-api.md):** Information on how tools are defined,
registered, and used by the core.
- **[Memory Import Processor](./memport.md):** Documentation for the modular
GEMINI.md import feature using @file.md syntax.
- **[Policy Engine](./policy-engine.md):** Use the Policy Engine for
- **[Core tools API](../reference/tools-api.md):** Information on how tools are
defined, registered, and used by the core.
- **[Memory Import Processor](../reference/memport.md):** Documentation for the
modular GEMINI.md import feature using @file.md syntax.
- **[Policy Engine](../reference/policy-engine.md):** Use the Policy Engine for
fine-grained control over tool execution.

## Role of the core
Expand Down Expand Up @@ -92,8 +92,8 @@ This allows you to have global, project-level, and component-level context
files, which are all combined to provide the model with the most relevant
information.

You can use the [`/memory` command](../cli/commands.md) to `show`, `add`, and
`refresh` the content of loaded `GEMINI.md` files.
You can use the [`/memory` command](../reference/commands.md) to `show`, `add`,
and `refresh` the content of loaded `GEMINI.md` files.

## Citations

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Expand Up @@ -17,7 +17,7 @@ the main agent's context or toolset.
> ```
>
> **Warning:** Subagents currently operate in
> ["YOLO mode"](../get-started/configuration.md#command-line-arguments), meaning
> ["YOLO mode"](../reference/configuration.md#command-line-arguments), meaning
> they may execute tools without individual user confirmation for each step.
> Proceed with caution when defining agents with powerful tools like
> `run_shell_command` or `write_file`.
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2 changes: 1 addition & 1 deletion docs/extensions/reference.md
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Expand Up @@ -130,7 +130,7 @@ The manifest file defines the extension's behavior and configuration.
- `description`: A short summary shown in the extension gallery.
- <a id="mcp-servers"></a>`mcpServers`: A map of Model Context Protocol (MCP)
servers. Extension servers follow the same format as standard
[CLI configuration](../get-started/configuration.md).
[CLI configuration](../reference/configuration.md).
- `contextFileName`: The name of the context file (defaults to `GEMINI.md`). Can
also be an array of strings to load multiple context files.
- `excludeTools`: An array of tools to block from the model. You can restrict
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