Bug: Stop hooks run with CWD set to .claude/helpers/ instead of project root

Description

Stop hooks execute with the current working directory set to .claude/helpers/ instead of the project root. This causes any relative paths in hook commands to resolve incorrectly.

Reproduction

1. Create a hook in .claude/settings.json:

{
  "hooks": {
    "Stop": [{
      "hooks": [{
        "type": "command",
        "command": "node .claude/helpers/my-hook.mjs sync",
        "timeout": 8000,
        "continueOnError": true
      }]
    }]
  }
}

1. Place my-hook.mjs at .claude/helpers/my-hook.mjs

1. End a session — the Stop hook fails with MODULE_NOT_FOUND because it resolves to .claude/helpers/.claude/helpers/my-hook.mjs (doubled path).

Expected Behavior

Stop hooks should run with CWD set to the project root (same as SessionStart hooks), so that relative paths like .claude/helpers/my-hook.mjs resolve correctly.

Actual Behavior

Stop hooks run with CWD = .claude/helpers/, causing relative paths to double:

• Expected: <project-root>/.claude/helpers/my-hook.mjs
• Actual: <project-root>/.claude/helpers/.claude/helpers/my-hook.mjs

Verification

# From project root — works
ls .claude/helpers/my-hook.mjs  # ✓ found

# From .claude/helpers/ (what Stop hooks see) — fails
cd .claude/helpers/
ls .claude/helpers/my-hook.mjs  # ✗ No such file or directory

Workaround

Use git rev-parse --show-toplevel to resolve the project root:

"command": "node \"$(git rev-parse --show-toplevel 2>/dev/null || echo .)/.claude/helpers/my-hook.mjs\" sync"

Impact

This affects any Stop hook that uses relative paths from the project root. The claude-flow init wizard generates stock settings.json with node .claude/helpers/auto-memory-hook.mjs sync in the Stop hook — which silently fails on every session end due to this bug (continueOnError: true masks the failure).

SessionStart hooks are not affected — they run with the correct CWD (project root).

Environment

• Claude Code: v2.1.39
• Platform: Linux 6.8.0-90-generic (x86_64)
• Node.js: v24.13.0