Docs: Refresh docs to organize and standardize reference materials. (#18403)

docs/cli/tutorials/shell-commands.md

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+# Execute shell commands
+
+Use the CLI to run builds, manage git, and automate system tasks without leaving
+the conversation. In this guide, you'll learn how to run commands directly,
+automate complex workflows, and manage background processes safely.
+
+## Prerequisites
+
+- Gemini CLI installed and authenticated.
+- Basic familiarity with your system's shell (Bash, Zsh, PowerShell, etc.).
+
+## How to run commands directly (`!`)
+
+Sometimes you just need to check a file size or git status without asking the AI
+to do it for you. You can pass commands directly to your shell using the `!`
+prefix.
+
+**Example:** `!ls -la`
+
+This executes `ls -la` immediately and prints the output to your terminal. The
+AI doesn't "see" this output unless you paste it back into the chat or use it in
+a prompt.
+
+### Scenario: Entering Shell mode
+
+If you're doing a lot of manual work, toggle "Shell Mode" by typing `!` and
+pressing **Enter**. Now, everything you type is sent to the shell until you exit
+(usually by pressing **Esc** or typing `exit`).
+
+## How to automate complex tasks
+
+You can automate tasks using a combination of Gemini CLI and shell commands.
+
+### Scenario: Run tests and fix failures
+
+You want to run tests and fix any failures.
+
+**Prompt:**
+`Run the unit tests. If any fail, analyze the error and try to fix the code.`
+
+**Workflow:**
+
+1.  Gemini calls `run_shell_command('npm test')`.
+2.  You see a confirmation prompt: `Allow command 'npm test'? [y/N]`.
+3.  You press `y`.
+4.  The tests run. If they fail, Gemini reads the error output.
+5.  Gemini uses `read_file` to inspect the failing test.
+6.  Gemini uses `replace` to fix the bug.
+7.  Gemini runs `npm test` again to verify the fix.
+
+This loop turns Gemini into an autonomous engineer.
+
+## How to manage background processes
+
+You can ask Gemini to start long-running tasks, like development servers or file
+watchers.
+
+**Prompt:** `Start the React dev server in the background.`
+
+Gemini will run the command (e.g., `npm run dev`) and detach it.
+
+### Scenario: Viewing active shells
+
+To see what's running in the background, use the `/shells` command.
+
+**Command:** `/shells`
+
+This opens a dashboard where you can view logs or kill runaway processes.
+
+## How to handle interactive commands
+
+Gemini CLI attempts to handle interactive commands (like `git add -p` or
+confirmation prompts) by streaming the output to you. However, for highly
+interactive tools (like `vim` or `top`), it's often better to run them yourself
+in a separate terminal window or use the `!` prefix.
+
+## Safety first
+
+Giving an AI access to your shell is powerful but risky. Gemini CLI includes
+several safety layers.
+
+### Confirmation prompts
+
+By default, **every** shell command requested by the agent requires your
+explicit approval.
+
+- **Allow once:** Runs the command one time.
+- **Allow always:** Trusts this specific command for the rest of the session.
+- **Deny:** Stops the agent.
+
+### Sandboxing
+
+For maximum security, especially when running untrusted code or exploring new
+projects, we strongly recommend enabling Sandboxing. This runs all shell
+commands inside a secure Docker container.
+
+**Enable sandboxing:** Use the `--sandbox` flag when starting the CLI:
+`gemini --sandbox`.
+
+## Next steps
+
+- Learn about [Sandboxing](../../cli/sandbox.md) to safely run destructive
+  commands.
+- See the [Shell tool reference](../../tools/shell.md) for configuration options
+  like timeouts and working directories.
+- Explore [Task planning](task-planning.md) to see how shell commands fit into
+  larger workflows.