SDK worktree creation contaminates parent repo's core.hooksPath config

Summary

The Claude Agent SDK's worktree creation logic writes core.hooksPath to the parent repository's .git/config without using the --worktree flag, causing the parent repo to lose access to the user's global git hooks.

Mechanism

In @anthropic-ai/claude-agent-sdk (versions 0.40.1 and 0.42.1 observed), the copyWorktreeIncludeFiles function searches for .husky or .git/hooks directories and writes their path to the worktree's config:

let Y = WN(q, ".husky"),
    A = WN(q, ".git", "hooks"),
    O = null;
for (let j of [Y, A]) try {
  if ((await Y85(j)).isDirectory()) { O = j; break }
} catch {}
if (O) {
  await M7(D7(), ["config", "core.hooksPath", O], { cwd: K });
}

Because git worktrees share .git/config with the parent repo by default (unless extensions.worktreeConfig is enabled), this command writes into the parent's config, overriding any user-configured global hooks with a path to the parent's stock .git/hooks directory.

Impact

When Claude Code creates a worktree from a parent repository:

• The parent repo's core.hooksPath is silently overwritten with /path/to/parent/.git/hooks
• User's global git hooks are disabled in the parent repo
• The path written typically contains only sample hook files, not functional hooks
• User discovers the issue only when hooks stop firing

Evidence

• SDK source locations: @anthropic-ai/claude-agent-sdk/cli.js function copyWorktreeIncludeFiles
• Observed behavior: Five Claude Code worktrees spawned from gmail_extension repo (May 11-14) correlate with observed core.hooksPath override
• Path written matches exactly: hooksPath = /Users/janac/Documents/GitHub/gmail_extension/.git/hooks
• Verified git pull/fetch/merge do NOT restore the override (ruled out as alternative cause)

Suggested Fix

1. Before creating worktrees, enable extensions.worktreeConfig=true on the parent repo:

``bash
git -C <parent_repo> config extensions.worktreeConfig true
``

1. Write core.hooksPath with the --worktree flag to isolate the config to the worktree only:

``javascript
await M7(D7(), ["config", "--worktree", "core.hooksPath", O], { cwd: K });
``

This ensures the hooks path applies only to the worktree and doesn't contaminate the parent repo's shared config.

Reproduction

1. Configure global git hooks via git config --global core.hooksPath <path>
2. Create a Claude Code worktree from any parent repo
3. Check the parent repo's config: git -C <parent_repo> config core.hooksPath
4. Observe the global hooks path has been replaced with <parent_repo>/.git/hooks

Environment

• Claude Code versions with SDK 0.40.1 and 0.42.1
• macOS (likely affects all platforms)
• Git 2.x with standard worktree configuration