> ## Documentation Index
> Fetch the complete documentation index at: https://commander-docs.cyshel.com/llms.txt
> Use this file to discover all available pages before exploring further.

# Agents

> Claude Code AI agents with full transparency and control.

## Overview

Agents are Claude Code SDK instances running within a workspace's git worktree. You see every message, tool call, file edit, and cost in real time.

## Starting Agents

Start an agent by writing a prompt in a workspace. You can run multiple agents per workspace for parallel tasks.

Each message supports per-message overrides:

| Option    | Values                                | Description                                                                |
| --------- | ------------------------------------- | -------------------------------------------------------------------------- |
| Model     | Default, Opus, Opus 1M, Sonnet, Haiku | Override the default model. Opus 1M uses a 1 million token context window. |
| Effort    | Low, Medium, High, Max                | Control thoroughness                                                       |
| Thinking  | On/Off                                | Extended thinking mode                                                     |
| Fast Mode | On/Off                                | Faster output                                                              |
| Plan Mode | On/Off                                | Step-by-step with approval                                                 |

## Lifecycle Controls

| Action         | Description                                                       |
| -------------- | ----------------------------------------------------------------- |
| **Pause**      | Suspend the agent, preserving session                             |
| **Resume**     | Continue from where it paused                                     |
| **Kill**       | Terminate immediately                                             |
| **Warmup**     | Pre-warm an agent session for faster response on the next message |
| **Rename**     | Change the agent's display name                                   |
| **Resume All** | Resume all paused agents across workspaces                        |
| **Rerun All**  | Create fresh agents for all workspace slots                       |

## Message Queue

When an agent is busy, messages are queued:

* Queued messages are persisted to SQLite (crash-safe)
* Auto-delivered when the agent becomes available
* Can be cancelled or force-delivered
* Each queued message preserves its model/effort/thinking/fast mode options
* Pending messages appear in a visual queue below the input area

## Plan Mode

When enabled, agents propose a step-by-step plan before executing:

1. Agent generates plan steps
2. You review and approve (or edit)
3. Agent executes approved steps
4. Progress tracked per-step

## Session Resumption

Agent sessions persist across app restarts:

* Session IDs stored in state
* On restart, agents with valid sessions resume automatically
* Agents without sessions are marked as errored with "Interrupted by app restart"
* Restart count is tracked per agent

## Token & Cost Tracking

Per-agent tracking includes:

* Input/output token counts
* Cache creation and read tokens
* Cost in USD (regular and overage costs tracked separately)
* Context window fill percentage with visual indicator
* Daily aggregate usage across all agents

Configure **Always Show Context Usage** in Settings to display the context fill percentage at all times. By default, it only appears when the context window is more than 70% full.

## Usage & Rate Limits

The status bar shows your Claude account usage and rate limit status:

* **Session (5hr)** — Rolling 5-hour token usage
* **Weekly** — 7-day aggregate usage
* **Weekly Opus / Weekly Sonnet** — Per-model weekly limits
* **Overage** — Usage beyond your subscription limits

Each bucket shows a utilization bar and resets-at time. Click the usage indicator in the status bar to see the full breakdown.

## Screenshot Sharing

Share visual context with agents:

* Capture screenshots using the global hotkey
* Drag and drop images into the message input
* Recent screenshots appear in a strip below the input
* Agents can reference screenshots when making decisions

## Question Cards

Agents and the manager can ask you structured questions:

* **Single choice** — Pick one option from a list
* **Multiple choice** — Select multiple options
* **Free text** — Type a response

Questions appear as interactive cards in the conversation. Answer directly or dismiss to skip.

## MCP Server Status

View the connection status of MCP servers configured for your repository:

* Connected, disconnected, or error states shown per server
* Click to view details or troubleshoot