Isolating Worktrees

Worktree Isolation

Overview

Git worktrees provide isolated workspaces, but Claude Code has characteristics that can cause changes to "bleed" to the wrong worktree:

1. cwd resets between Bash calls - Each Bash tool invocation starts in the original working directory
2. Subagents don't inherit verified context - They start with zero knowledge of parent's location
3. No automatic verification - Nothing enforces you're in the right place before git operations

This skill provides protocols to ensure ALL changes stay in the intended worktree.

The Problem

Why Changes Bleed

# WRONG - This DOES NOT work in Claude Code
cd /path/to/worktree
git status  # This runs in ORIGINAL directory, not worktree!

Each Bash tool call is independent. The cd command affects only that shell session, which ends immediately. The next Bash call starts fresh in the original working directory.

Subagent Context Loss

When you spawn a subagent with:

Work from: /path/to/worktree

This is just text. The subagent has no verified context about which directory it should use. If it runs git commit, it commits wherever Claude Code's process is running - likely your main branch.

The Solution: Verification Protocol

Rule 1: Always Chain Commands

WRONG:

cd /path/to/worktree
git add .
git commit -m "message"

RIGHT:

cd /path/to/worktree && git add . && git commit -m "message"

Or use git's -C flag:

git -C /path/to/worktree add .
git -C /path/to/worktree commit -m "message"

Rule 2: Verify Before Every Git Operation

Before ANY git write operation (add, commit, push, merge, etc.), run verification:

cd /path/to/worktree && \
  echo "=== WORKTREE VERIFICATION ===" && \
  echo "Current directory: $(pwd)" && \
  echo "Git root: $(git rev-parse --show-toplevel)" && \
  echo "Branch: $(git branch --show-current)" && \
  echo "Expected: /path/to/worktree on branch-name" && \
  echo "============================"

STOP if verification fails. Do not proceed with git operations.

Rule 3: Use Absolute Paths Everywhere

Never use relative paths in worktree contexts:

WRONG:

git add src/file.ts

RIGHT:

git -C /absolute/path/to/worktree add src/file.ts

Rule 4: Subagent Prompts MUST Include Verification

When dispatching subagents for worktree work, include this verification block:

## CRITICAL: Working Directory Verification

You are working in worktree: /absolute/path/to/worktree
Expected branch: feature-branch-name

**BEFORE making ANY changes, run this verification:**

```bash
cd /absolute/path/to/worktree && \
  echo "VERIFICATION:" && \
  echo "Directory: $(pwd)" && \
  echo "Git root: $(git rev-parse --show-toplevel)" && \
  echo "Branch: $(git branch --show-current)"

Expected output:

• Directory: /absolute/path/to/worktree
• Git root: /absolute/path/to/worktree
• Branch: feature-branch-name

If ANY value doesn't match, STOP immediately and report the mismatch.

For ALL git commands, use this pattern:

cd /absolute/path/to/worktree && git [command]

## Implementation Pattern

### Setting Up a Worktree for Implementation

```bash
# 1. Create the worktree
WORKTREE_PATH="$(pwd)/.worktrees/feature-name"
BRANCH_NAME="feature/feature-name"

git worktree add "$WORKTREE_PATH" -b "$BRANCH_NAME"

# 2. Verify creation
git worktree list | grep "$WORKTREE_PATH"

# 3. Install dependencies (chained!)
cd "$WORKTREE_PATH" && npm install && npm test

# 4. Store the absolute path for subagents
echo "Worktree ready at: $WORKTREE_PATH"

Dispatching Subagents for Worktree Work

When using the Task tool for work in a worktree:

Tool: Task
Description: "Implement feature X in worktree"
Prompt: |
  You are implementing [task] in an isolated git worktree.

  ## CRITICAL: Working Directory Context

  **Worktree location:** /Users/sam/project/.worktrees/feature-name
  **Branch:** feature/feature-name
  **Main repo:** /Users/sam/project (DO NOT modify)

  ### Verification (RUN FIRST)

  Before ANY work, verify your location:

  ```bash
  cd /Users/sam/project/.worktrees/feature-name && \
    echo "Directory: $(pwd)" && \
    echo "Git root: $(git rev-parse --show-toplevel)" && \
    echo "Branch: $(git branch --show-current)"

Expected:

• Directory: /Users/sam/project/.worktrees/feature-name
• Git root: /Users/sam/project/.worktrees/feature-name
• Branch: feature/feature-name

If verification fails, STOP and report. Do not proceed.

Command Pattern

ALL commands must use this pattern:

cd /Users/sam/project/.worktrees/feature-name && [your command]

Examples:

• Run tests: cd /Users/sam/project/.worktrees/feature-name && npm test
• Git status: cd /Users/sam/project/.worktrees/feature-name && git status
• Commit: cd /Users/sam/project/.worktrees/feature-name && git add . && git commit -m "message"

Your Task

[Task description here]

Report Back

Include in your report:

1. Verification output (proving you worked in correct worktree)
2. Final git status from worktree
3. Commit hash of your changes

### Verifying Subagent Work

After a subagent completes, verify their work landed in the right place:

```bash
# Check the worktree has the commits
cd /path/to/worktree && git log --oneline -5

# Verify main branch was NOT modified
cd /path/to/main/repo && git log --oneline -5
# Should NOT contain subagent's commits

Common Mistakes

Mistake 1: Trusting Inherited Context

Problem: Assuming subagent is in the right directory Solution: Always include explicit verification in subagent prompts

Mistake 2: Separate Bash Calls

Problem:

cd /worktree
git status  # WRONG - runs in original directory

Solution:

cd /worktree && git status  # RIGHT - chained

Mistake 3: Relative Paths

Problem:

git add src/file.ts  # Where does this run?

Solution:

git -C /absolute/worktree/path add src/file.ts

Mistake 4: Missing Verification in Subagent Prompts

Problem: Work from: /path/to/worktree is just documentation

Solution: Include verification commands and expected output in prompt

Integration with implementing-issue Skill

When using the implementing-issue skill with worktrees:

Setup Phase Addition

Before dispatching any implementation subagents:

# Store worktree path as absolute
WORKTREE_PATH="$(cd /path/to/worktree && pwd)"
echo "Using worktree: $WORKTREE_PATH"

# Verify it's actually a worktree
git -C "$WORKTREE_PATH" rev-parse --is-inside-work-tree
git -C "$WORKTREE_PATH" worktree list | grep "$WORKTREE_PATH"

Subagent Prompt Template

Replace the generic Work from: [current directory] with:

## Working Directory (CRITICAL)

**Worktree:** [ABSOLUTE_WORKTREE_PATH]
**Branch:** [BRANCH_NAME]

### Mandatory Verification (run before any work)

```bash
cd [ABSOLUTE_WORKTREE_PATH] && \
  echo "Location: $(pwd)" && \
  echo "Branch: $(git branch --show-current)" && \
  test "$(pwd)" = "[ABSOLUTE_WORKTREE_PATH]" && \
  echo "VERIFIED" || echo "VERIFICATION FAILED - STOP"

Command Pattern

All commands MUST follow this pattern:

cd [ABSOLUTE_WORKTREE_PATH] && [command]

DO NOT run any git commands without the cd && prefix.

### Completion Verification

After all subagents complete, verify isolation was maintained:

```bash
# 1. Check worktree has expected commits
echo "=== Worktree commits ===" && \
cd /path/to/worktree && git log --oneline -10

# 2. Check main branch was NOT modified
echo "=== Main branch commits (should be unchanged) ===" && \
cd /path/to/main && git log --oneline -5

# 3. Verify no uncommitted changes in main
cd /path/to/main && git status --short

Quick Reference

Red Flags

STOP if you see:

• Subagent prompt says "Work from:" without verification commands
• Git commands without -C flag or cd && prefix
• Verification shows wrong directory or branch
• Commits appearing in main branch unexpectedly
• Subagent didn't include verification output in report

ALWAYS:

• Use absolute paths
• Chain commands with &&
• Include verification in subagent prompts
• Verify subagent work landed in correct worktree
• Check main branch wasn't modified

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