clean-worktrees

A project command that removes Git worktrees belonging to branches already merged into the default branch, usually main or master.

In plain words
What is it for?
Use it to find and remove merged worktrees, prune stale Git worktree references, or preview what would be removed with --dry-run.
Why use it?
It clears obsolete working directories after their branches are merged, reducing clutter from completed work. Dry-run mode lets you preview the removals first.

Command for Claude Code

Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

agentmods
npx agentmods add commands/brain-bootstrap/claude-code-brain-bootstrap/clean-worktrees
Clone the repo
git clone --depth 1 https://github.com/brain-bootstrap/claude-code-brain-bootstrap

Made for: Claude Code.

Per session 18 Only the description is in the session, so the agent can decide to use it. The body loads when it is invoked.
When invoked 1,221 The whole file, excluding the scripts and references it only reads on demand.
Security scan C 1 finding. Scan, not verified.
Origin original No closer match found in the catalogue.
Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

ModelPer sessionOnce invoked
Fable 5 $0.00018 $0.01221
Opus 5 $0.00009 $0.00611
Sonnet 5 $0.00004 $0.00244
Haiku 4.5 $0.00002 $0.00122

Measured 2d ago against content hash b7aa1940100b, method: parsed. Prices are Anthropic first-party input rates as of 2026-08-30, from the pricing page.

Security

Grade C, and why

clean-worktrees scanned grade C with 1 finding against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 2d ago.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Recursive force deletehighDestructive command

rm -rf with a variable or a broad path is one typo away from removing the wrong tree.

rm -rf "$path" 2>/dev/null || true
.claude/commands/clean-worktrees.md · 170 lines

How it starts

The opening of the file, as written. The whole thing — 170 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Clean Worktrees (Automatic)

Automatically remove all worktrees for branches merged into the default branch (main or master). No interaction required.

Usage

/clean-worktrees              # Remove all merged worktrees
/clean-worktrees --dry-run    # Preview what would be deleted

Implementation

Execute this script:

#!/bin/bash
set -euo pipefail

DRY_RUN=false
if [[ "${ARGUMENTS:-}" == *"--dry-run"* ]]; then
  DRY_RUN=true
fi

# Detect default branch (main or master)
DEFAULT_BRANCH=$(git symbolic-ref refs/remotes/origin/HEAD 2>/dev/null | sed 's|.*/||' || \
                 git branch --list main master 2>/dev/null | head -1 | xargs || \
                 echo "main")

echo "Cleaning Worktrees"
echo "=================="
echo "Default branch: $DEFAULT_BRANCH"
echo ""

# Step 1: Prune stale git references
echo "1. Pruning stale git references..."
PRUNED=$(git worktree prune -v 2>&1)
if [ -n "$PRUNED" ]; then
  echo "$PRUNED"
  echo "Stale references pruned"
else
  echo "No stale references found"
fi
echo ""

# Step 2: Find merged worktrees
echo "2. Finding merged worktrees..."
MERGED_COUNT=0
MERGED_BRANCHES=()
CURRENT_DIR="$(pwd)"

while IFS= read -r line; do
  path=$(echo "$line" | awk '{print $1}')
  branch=$(echo "$line" | grep -oE '\[.*\]' | tr -d '[]' || true)

  [ -z "$branch" ] && continue
  [ "$branch" = "master" ] && continue
  [ "$branch" = "main" ] && continue
  [ "$path" = "$CURRENT_DIR" ] && continue

  if git branch --merged "$DEFAULT_BRANCH" 2>/dev/null | grep -q "^[* ] ${branch}$"; then
    MERGED_COUNT=$((MERGED_COUNT + 1))
    MERGED_BRANCHES+=("$branch|$path")
    echo "  - $branch (merged)"
  fi
done < <(git worktree list)

if [ $MERGED_COUNT -eq 0 ]; then
  echo "No merged worktrees found"
  echo ""
  echo "Current worktrees:"
  git worktree list
  exit 0
fi

echo ""
echo "Found $MERGED_COUNT merged worktree(s)"
echo ""

if [ "$DRY_RUN" = true ]; then
  echo "DRY RUN - No changes will be made"
  echo ""
  echo "Would delete:"
  for item in "${MERGED_BRANCHES[@]}"; do
    branch=$(echo "$item" | cut -d'|' -f1)
    path=$(echo "$item" | cut -d'|' -f2)
    echo "  - $branch"
    echo "    Path: $path"
  done
  echo ""
  echo "Run without --dry-run to actually delete"
  exit 0
fi

# Step 3: Remove merged worktrees
echo "3. Removing merged worktrees..."
REMOVED_COUNT=0

for item in "${MERGED_BRANCHES[@]}"; do
  branch=$(echo "$item" | cut -d'|' -f1)
  path=$(echo "$item" | cut -d'|' -f2)

  echo ""
  echo "Removing: $branch"

  if git worktree remove "$path" 2>/dev/null; then
    echo "  Worktree removed"
  else
    echo "  Git remove failed, forcing..."
    rm -rf "$path" 2>/dev/null || true
    git worktree prune 2>/dev/null || true
    echo "  Worktree forcefully removed"
  fi

  if git branch -d "$branch" 2>/dev/null; then
    echo "  Local branch deleted"
  else
    echo "  Local branch already deleted"
  fi

  if git ls-remote --heads origin "$branch" 2>/dev/null | grep -q "$branch"; then
    echo "  Remote branch exists: origin/$branch (not auto-deleted)"
  fi

  REMOVED_COUNT=$((REMOVED_COUNT + 1))
done

echo ""
echo "Cleanup complete"
echo ""
echo "Summary:"
echo "  Removed: $REMOVED_COUNT worktree(s)"
echo ""
echo "Remaining worktrees:"
git worktree list
echo ""

WORKTREES_SIZE=$(du -sh .worktrees/ 2>/dev/null | awk '{print $1}' || echo "N/A")
echo "Worktrees disk usage: $WORKTREES_SIZE"

Read the full file on GitHub · 170 lines

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

  1. 2d ago First seen · 170 lines · 18 tokens per session scan C b7aa1940100b

Subscribe to this mod's changes

clean-worktrees is a command published in the GitHub repository brain-bootstrap/claude-code-brain-bootstrap (11 stars, last pushed 4mo ago), licensed MIT. It adds 18 tokens to every session and 1,221 once invoked, about $0.0001 per session on Opus 5. A static security scan graded it C with 1 finding (recursive force delete). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.