[kixelated]

Summary

• Initialize submodules before returning a new worktree. Clone and remote verification run outside the registry lock while the reservation remains charged; a creator record distinguishes live creation from interrupted recovery.
• Keep remotely verified module tips under refs/remotes/quest-pins/, outside origin's branch-prune namespace. Fetch cloned tags by name, then batch any remaining SHA-only tips. This preserves fetched pins and tags without treating a pushed superproject gitlink as an uploaded module object.
• Check module files and every module store, including deinitialized ones, before removal. Nested scratch uses its module's ignore rules. Protect leftover deinitialized files and local commits made after creation. Refuse removal while a module store has linked worktrees of its own, which deleting the store would break.
• Charge each checkout's module stores, cloned into its own Git directory outside its path, in the disk budget; the derived reserve includes the main checkout's module stores.
• Route nested hook cwds through the selected project while preserving direct vendored-project sessions and unrelated-cwd behavior.
• Run every Git subprocess in worktree.ts and worktree-hook.ts without the repository-local variables (git rev-parse --local-env-vars, keeping -c config as Git does for other repositories). A Git hook or git submodule foreach exports GIT_DIR/GIT_WORK_TREE, which override -C discovery: with them naming a submodule, the hook created the worktree inside the submodule and removal checks inspected the wrong repository.

Claude Code's standard WorktreeCreate hook is the immediate consumer. This adds module support without a new post-create configuration API.

Merged with main after moq-dev/quest#425 landed, keeping both behaviors: a subagent hook walks up from a submodule cwd to the first registered checkout, then applies #425's agent-<id> match or workflow-agent binding; WorktreeCreate fetches a pr-<number> head through the project-routed checkout, falling back to the default base. Main's new gate-scope tests now await this PR's async run fixture, and a regression test binds a workflow agent that starts inside a submodule of its checkout.

Checks

• just check and just test pass on adb28aa66f4b8cbf9a8a5087d930795b7b4b0a48: 1001 CLI tests, 2 skipped; 508 Worker tests; bundled/native lifecycle and shell suites.
• New regression tests fail on the head before the module fixes: the hook under inherited GIT_DIR/GIT_WORK_TREE/GIT_INDEX_FILE created repo/sub/.worktrees/agent-located; a 1 MiB module store went uncharged (allocated 1073152); removal deleted a module store serving a linked worktree.
• Real isolated public-remote fixture passes create, first devshell, owner/non-owner stop, restore, and removal, preserving parent scratch (on c30efe23dd17bada5561d7c6a0d850548ee9a5c6; not rerun).
• Fixture temporary directories stay under the checkout, with a Git discovery ceiling for outside-repository cases.

Review

• Codex, GPT-6.1 Sol, medium effort, via quest review --base origin/main --harness codex --new (Claude Code authored the latest commits).
• Round 3 reviewed 66bdaab61e9525b7cefb5126e34d0b854096fc21, the hand-resolved merge with main (moq-dev/quest#425) plus the test fixes: no findings. The pushed head adb28aa66f4b8cbf9a8a5087d930795b7b4b0a48 adds only a conflict-free merge of main (moq-dev/quest#439, moq-dev/quest#407).
• Round 2 reviewed 0a54dd00ba5b0361fa3d4e08d003f5f3ff1fd8be: no findings.
• Round 1 on 24cc9ebf2521cf73284627a014e5abfee0f0716b, both fixed: module stores were outside disk-budget accounting; removal could delete a module store serving another worktree.
• CodeRabbit's inherited Git location variables finding: fixed.
• Earlier rounds (Claude Code, Claude Opus 5.5, on c30efe23dd17bada5561d7c6a0d850548ee9a5c6) fixed clone locking, live-creator state, nested scratch and Windows paths, hook project routing, fetched-tip preservation, deinitialized files, and recovery advice. Accepted refutations: malformed module metadata fails closed; removal requires exclusive ownership and cannot fence arbitrary unsupervised writers. Git's required force flag is used only after recursive safety checks.

(Written by GPT-6.1 Sol and Claude Opus 5.5)

🤖 Generated with Claude Code

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Commits

Reviewing files that changed from the base of the PR and between 5e6b104 and adb28aa.

Files selected for processing: 7

• README.md
• src/cli/main.ts
• src/cli/worktree-hook.ts
• src/cli/worktree.ts
• test/agent.test.ts
• test/worktree.run.test.ts
• test/worktree.test.ts

Walkthrough

Worktree creation is now asynchronous and initializes submodules recursively. Removal checks root and submodule files, ignored paths, and commits in module stores before deleting a checkout. Hook checkout resolution now walks enclosing superprojects and can use an explicit project root. CLI creation uses shared promise handling. Tests were updated for asynchronous operations and expanded to cover nested submodule creation, preservation, and removal checks.

Merge Risk: Moderate · previous review 5e6b1

A hook launched with inherited Git location variables can create a worktree in the wrong repository. Clear those variables for Git subprocesses before merging.

Pre-merge checks: 4 · 1

Failed checks: 1 warning

Check name	Status	Explanation	Resolution
Docstring Coverage		Docstring coverage is 75.00% which is insufficient. The required threshold is 80.00%. Docstring coverage is scoped to functions touched by this diff with cyclomatic complexity of at least 2. Documenta…	Write docstrings for the functions missing them to satisfy the coverage threshold.

Passed checks: 4 passed

Check name	Status	Explanation
Title check		The title "fix(worktree): initialize submodules and preserve their local work" matches the main change. The raw summary and objectives show recursive submodule initialization during worktree creation,…
Linked Issues check		Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check		Check skipped because no linked issues were found for this pull request.
Description check		The description is clearly related to the changeset. It describes submodule initialization during worktree creation, submodule-aware removal checks, module-store disk budget accounting, hook project r…

Full details: Title check

Explanation

The title "fix(worktree): initialize submodules and preserve their local work" matches the main change. The raw summary and objectives show recursive submodule initialization during worktree creation, plus recursive checks before removal so local submodule work is preserved. The title is concise, specific, and follows a conventional commit style.

Full details: Description check

Explanation

The description is clearly related to the changeset. It describes submodule initialization during worktree creation, submodule-aware removal checks, module-store disk budget accounting, hook project routing, and the Git environment-variable fix. It also lists the test results and review rounds, so it is specific rather than vague.

Full details: Docstring Coverage

Explanation

Docstring coverage is 75.00% which is insufficient. The required threshold is 80.00%. Docstring coverage is scoped to functions touched by this diff with cyclomatic complexity of at least 2. Documentation-only edits and deletions within surviving functions are included; unchanged diff context and fully deleted functions are excluded. Analyzed 8 functions across 6 files. (1 skipped: 1 unsupported.)

Resolution

Write docstrings for the functions missing them to satisfy the coverage threshold.

Finishing Touches

Simplify code

• Commit to this branch
• Create a new PR

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Commits

Reviewing files that changed from the base of the PR and between acb8682 and 5e6b104.

Files selected for processing: 7

• README.md
• src/cli/main.ts
• src/cli/worktree-hook.ts
• src/cli/worktree.ts
• test/agent.test.ts
• test/worktree.run.test.ts
• test/worktree.test.ts

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[kixelated]

Design change: A real submodule fixture reached its first devshell and stop/restore, but clean removal refused an object reachable through a cloned tag but no remote-tracking branch. Initialization fetched that tag from the remote without a separate remote-tracking ref. Preserve that signal at creation: when a new module has a tip not remotely tracked, explicitly verify that tip by fetching it to a namespaced remote-tracking ref outside origin's branch-prune refspec. Continue refusing later local commits. This verifies the object at its source; it does not trust a superproject gitlink as preservation. Add a fixture for remote-fetched refs absent from branches, then repeat both gates and a new local review.

(Written by GPT-6.1 Sol)