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Auto Run is a file-system-based document runner that lets you process tasks using AI agents. Select a folder containing markdown documents with task checkboxes, and Maestro will work through them one by one, spawning a fresh AI session for each task. Auto Run

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Setting Up Auto Run

  1. Navigate to the Auto Run tab in the right panel (Cmd+Shift+1)
  2. Select a folder containing your markdown task documents
  3. Each .md file becomes a selectable document

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Creating Tasks

Use markdown checkboxes in your documents: 
# Feature Implementation Plan

- [ ] Implement user authentication
- [ ] Add unit tests for the login flow
- [ ] Update API documentation
Tip: Press Cmd+L (Mac) or Ctrl+L (Windows/Linux) to quickly insert a new checkbox at your cursor position.

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Running Single Documents

  1. Select a document from the dropdown
  2. Click the Run button (or the ▶ icon)
  3. Customize the agent prompt if needed, then click Go

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Running Multiple Auto Run Documents

Auto Run supports running multiple documents in sequence:
  1. Click Run to open the Auto Run configuration modal
  2. Click + Add Docs to add more documents to the queue
  3. Drag to reorder documents as needed
  4. Configure options per document:
    • Reset on Completion - Creates a working copy in Runs/ subfolder instead of modifying the original. The original document is never touched, and working copies (e.g., TASK-1735192800000-loop-1.md) serve as audit logs.
    • Duplicate - Add the same document multiple times
  5. Enable Loop Mode to cycle back to the first document after completing the last
  6. Click Go to start running documents

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Playbooks

Save your Auto Run configurations as Playbooks for reuse:
  1. Configure your documents, order, and options
  2. Click Save as Playbook and enter a name
  3. Load saved playbooks from the Load Playbook dropdown
  4. Update or discard changes to loaded playbooks
Playbooks

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Inline Wizard

Generate new playbooks from within an existing session using the Inline Wizard:
  1. Type /wizard in any AI tab (or click the Wizard button in the Auto Run panel)
  2. Have a conversation with the AI about your project goals
  3. Watch the confidence gauge build as the AI understands your requirements
  4. At 80%+ confidence, the AI generates detailed Auto Run documents
Inline Wizard The Inline Wizard creates documents in a unique subfolder under your Auto Run folder, keeping generated playbooks organized. When complete, your tab is renamed to reflect the project and you can immediately start running the generated tasks.

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Playbook Exchange

Looking for pre-built playbooks? The Playbook Exchange offers community-contributed playbooks for common workflows like security audits, code reviews, and documentation generation. Open it via Quick Actions (Cmd+K) or click the Exchange button in the Auto Run panel.

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Progress Tracking

The runner will:
  • Process tasks serially from top to bottom
  • Skip documents with no unchecked tasks
  • Show progress: “Document X of Y” and “Task X of Y”
  • Mark tasks as complete (- [x]) when done
  • Log each completion to the History panel

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Session Isolation

Each task executes in a completely fresh AI session with its own unique session ID. This provides:
  • Clean context - No conversation history bleeding between tasks
  • Predictable behavior - Tasks in looping playbooks execute identically each iteration
  • Independent execution - The agent approaches each task without memory of previous work
This isolation is critical for playbooks with Reset on Completion documents that loop indefinitely. Each loop creates a fresh working copy from the original document, and the AI approaches it without memory of previous iterations.

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Environment Variables

Maestro sets environment variables that your agent hooks can use to customize behavior:
VariableValueDescription
MAESTRO_SESSION_RESUMED1Set when resuming an existing session (not set for new sessions)
Example: Conditional Hook Execution Since Maestro spawns a new agent process for each message (batch mode), agent “session start” hooks will run on every turn. Use MAESTRO_SESSION_RESUMED to skip hooks on resumed sessions: 
# In your agent's session start hook
[ "$MAESTRO_SESSION_RESUMED" = "1" ] && exit 0
# ... rest of your hook logic for new sessions only
This works with any agent provider (Claude Code, Codex, OpenCode) since the environment variable is set by Maestro before spawning the agent process.

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History & Tracking

Each completed task is logged to the History panel with:
  • AUTO label indicating automated execution
  • Session ID pill (clickable to jump to that AI conversation)
  • Summary of what the agent accomplished
  • Full response viewable by clicking the entry
Keyboard navigation in History:
  • Up/Down Arrow - Navigate entries
  • Enter - View full response
  • Esc - Close detail view and return to list

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Expanded Editor View

For editing complex Auto Run documents, use the Expanded Editor — a fullscreen modal that provides more screen real-estate. To open the Expanded Editor:
  • Click the expand icon (↗️) in the top-right corner of the Auto Run panel
  • Or press Cmd+Shift+E (Mac) / Ctrl+Shift+E (Windows/Linux) to toggle
Expanded Auto Run Editor The Expanded Editor provides:
  • Edit/Preview toggle — Switch between editing markdown and previewing rendered output
  • Document selector — Switch between documents without closing the modal
  • Run controls — Start, stop, and monitor Auto Run progress from the expanded view
  • Task progress — See “X of Y tasks completed” and token count at the bottom
  • Full toolbar — Create new documents, refresh, and open folder
Click Collapse or press Esc to return to the sidebar panel view.

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Saving Documents

Save your changes with Cmd+S (Mac) or Ctrl+S (Windows/Linux), or click the Save button in the editor footer. The editor shows “Unsaved changes” and a Revert button when you have pending edits. Full undo/redo support with Cmd+Z / Cmd+Shift+Z. Note: Switching documents discards unsaved changes. Save before switching if you want to preserve your edits.

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Image Support

Paste images directly into your documents. Images are saved to an images/ subfolder with relative paths for portability.

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Stopping the Runner

Click the Stop button at any time. The runner will:
  • Complete the current task before stopping
  • Preserve all completed work
  • Allow you to resume later by clicking Run again

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Parallel Auto Runs

Auto Run can execute in parallel across different agents without conflicts — each agent works in its own project directory, so there’s no risk of clobbering each other’s work. Same project, parallel work: To run multiple Auto Runs in the same repository simultaneously, create worktree sub-agents from the git branch menu (see Git Worktrees). Each worktree operates in an isolated directory with its own branch, enabling true parallel task execution on the same codebase.

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Run in Worktree

You can dispatch an Auto Run directly into a new git worktree from the run configuration modal. This spins up an isolated branch and directory for the entire run, keeping your main working tree clean. Run in Worktree
OptionDescription
Dispatch to a separate worktreeToggle to enable worktree isolation for this run
Worktree selectionCreate a new worktree or select an existing one
Base BranchThe branch to base the new worktree on (e.g., main)
Worktree Branch NameName for the new branch — also used as the worktree directory name
Automatically create PRWhen checked, Maestro opens a pull request from the worktree branch when the run completes
This is the recommended workflow for longer Auto Runs — your main branch stays untouched, all changes land on a dedicated branch, and you get a PR at the end ready for review.