Baton writes a few things into your repo. Most of it is local runtime state that should never be committed — especially the task worktrees under .baton/, which are full working copies of your repo. This page tells you exactly what to ignore and what to keep.

The .gitignore block

Paste this into your repo's .gitignore:

.gitignore

# Baton — local runtime state (worktrees, tasks, history, memory, reports, temp)
.baton/

# Generated knowledge graphs (rebuild with `baton kb init`)
graphify-out/

# Machine-specific MCP config (absolute paths; regenerate with `baton kb init`)
.mcp.json

# Recommended: Cursor's per-machine MCP config
.cursor/mcp.json

Always ignore .baton/

.baton/wt/ contains a git worktree per task — a full checkout of your repo. Committing it would add thousands of duplicate files. .baton/ must always be gitignored.

What's committed vs ignored

Artifact	Path	Why
Task worktrees	`.baton/wt/<slug>/`	Full per-task checkouts — local only
Task registry	`.baton/tasks.json`	Machine-specific daemon state
History DB	`.baton/history.db`	Local SQLite history
Project memory	`.baton/memory/facts/`	Shared per-machine, not per-clone
Merge reports	`.baton/reports/`	Local completion reports
Temp files	`.baton/tmp/`	Transient
Handoff briefs	`.baton/wt/<slug>/HANDOFF.md`	Inside the worktree
Graphify output	`graphify-out/`	Generated; rebuild with `baton kb rebuild`
MCP config	`.mcp.json`, `.cursor/mcp.json`	Contain machine-specific absolute paths

Artifact	Why commit it
`CODEBASE.md`	The token-cheap map; teammates skip re-indexing
`baton.config.json`	Routing rules — team-shared, deterministic
`AGENTS.md`	Coordination guide for agents (Baton appends a section)
`.graphifyignore`	Tells graphify what to skip
`kb/` (if `baton kb share on`)	The portable knowledge base so others clone-and-go

Reclaim junk you already have

If worktrees, branches, tmux sessions, or temp files pile up (interrupted runs, manual deletes), audit and reclaim them:

baton doctor              # read-only: lists orphaned worktrees, branches, tmux, temp files
baton clean               # dry-run: shows what WOULD be removed
baton clean --fix         # actually reclaim it
baton clean --fix --force # also remove worktrees with uncommitted changes

Safe by default

baton clean is a dry-run until you add --fix, and it never deletes a worktree with uncommitted changes unless you add --force. The daemon also sweeps only provably-dead temp files on startup — never your worktrees.

Keep Your Repo Clean

The .gitignore block

What's committed vs ignored

Reclaim junk you already have

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