Git Repo#

Git repository management and SourceGit GUI client integration.

Topics#

TopicDescriptionGuidecloneghq get with automatic SourceGit registration (multi-account support)clone.mdconflict-dry-runtest merge/cherry-pick applicability in an isolated worktree, without touching the main working treeconflict-dry-run.mdcredential-helperpin a per-org GitHub token for HTTPS remotes (fixes recurring Repository not found from active-account mismatch); HTTPS counterpart to ssh-keycredential-helper.mddoctordiagnose Git repository hook health, wiring, permissions, and CI compliance (Base universal + Conditional domain/type taxonomy; helper: scripts/git-repo-doctor.sh)doctor.mdfix-worktreebare repo worktree configuration recoveryfix-worktree.mdgithooksdiagnose a .githooks/ hook that silently never runs (hooksPath precedence, passthrough chains, execute bit) and choose an install method that keeps machine-wide hooksgithooks.mdisolate-hunkstage only your own edit when a tracked file's working tree mixes it with unrelated uncommitted content, via git plumbing (no working-tree changes)isolate-hunk.mdmerge-duplicatemerge duplicate repositories with the same originmerge-duplicate.mdmigraterenamed → to-ghq (backward-compat alias)migrate.mdmove-worktreemove/register unregistered worktrees to .claude/worktrees/, reclaim merged PR worktreesmove-worktree.mdpatrolbatch inspection of ghq repositories (status, stash, unpushed + commit-splitter integration)patrol.mdrebase-auditaudit an active interactive rebase's staged files for accidental reverts (HEAD-vs-index diff + revert-pattern heuristic + AskUserQuestion multiSelect) without touching the rebase itselfrebase-audit.mdrename-worktreerename worktree directory and metadata (cross-platform, Windows safe)rename-worktree.mdsafe-relocaterelocate working commits from a stale, diverged, or dirty branch onto a clean branch cut directly off the latest remote base (5-step procedure)safe-relocate.mdsourcegitSourceGit preference.json management (add repos, workspaces, folder rename)sourcegit.mdssh-keyper-repo SSH key mapping for multi-account GitHub (core.sshCommand + IdentityAgent)ssh-key.mdto-bareconvert a regular repo → bare + worktree at a custom location, preserving uncommitted changes (inverse of to-ghq; helper: scripts/repo-to-bare-worktree.sh)to-bare.mdto-ghqmigrate bare+worktree → regular .git at the ghq path (formerly migrate)to-ghq.mdworktreeunified worktree acquisition: inventory, reuse inactive, or create new at .claude/worktrees/worktree.mdworktree-drift-syncre-verify each worktree's git state immediately before/after applying an identical fix across a repo's multiple worktrees under external concurrent editingworktree-drift-sync.mdworktree-registershared: register a populated directory as a worktree via metadata only (used by fix-worktree + to-bare)worktree-register.md

Topic Dependencies#

text

worktree (entry point — inventory + decision)
  └─→ rename-worktree (reuse registered worktree)
  └─→ move-worktree (register unregistered or relocate)

worktree-register (shared metadata register/relink mechanism)
  ├─← fix-worktree (recover a broken bare-worktree link)
  └─← to-bare (link the working tree after a regular→bare conversion)

to-bare  ←inverse→  to-ghq (formerly `migrate`)

ssh-key (SSH multi-account)  ──counterpart──  credential-helper (HTTPS multi-account)

rebase-audit (active-rebase revert detection)  ──restoration mechanism shared with──  isolate-hunk (targeted hunk staging)

Worktree decision tree (HARD STOP — every time a worktree is needed)#

Whenever a worktree is needed (plan/build/test without switching branches, PR verification, isolated work environment, new commit while main branch has another in-flight task), check for inactive worktree reuse before creating a new one.

Flow#

1. git -C <repo> worktree list to enumerate existing worktrees

2. Operation-state gate (HARD STOP — before any inactive classification): for each candidate worktree <W>, check for an in-progress git operation: bash

   gitdir=$(git -C <W> rev-parse --absolute-git-dir)
   ls "$gitdir"/CHERRY_PICK_HEAD "$gitdir"/MERGE_HEAD "$gitdir"/REBASE_HEAD "$gitdir"/BISECT_LOG "$gitdir"/rebase-merge "$gitdir"/rebase-apply 2>/dev/null
   git -C <W> status --porcelain | grep -E '^(DD|AU|UD|UA|DU|AA|UU)'   # unmerged index entries
   
   

   Any hit = a cherry-pick/merge/rebase/bisect is mid-flight (likely the user's active operation) → the worktree is NOT an inactive candidate, its dirty files are the operation's payload (never offer discard / git add resolution / stash), and reuse is forbidden — report to the user instead. Merge-status heuristics (branch merged + ahead=0) do NOT override this gate. (see failed-attempts.md "cherry-pick in progress misclassified as abandoned")

3. Identify inactive candidates (only among worktrees that passed the gate):

   • Merged-PR worktrees (commit hash equals the base branch's merge commit)
   • Squash-merged-PR worktrees — see the caveat below; the hash test above does not find these
   • Stale fix/refactor branch worktrees (confirm with the user)

Hash-equality misses every squash merge (HARD STOP): a squash merge creates a new single commit on the base with no parent link to the branch, so a worktree whose PR was squashed keeps a HEAD that matches nothing on the base. The test in the first bullet reports it as not merged, and its N original commits still read as unmerged work — which both hides a reclaimable worktree and, worse, makes a genuinely stale branch look active. Ask GitHub for the PR state instead of inferring it from hashes: bash

B=$(git -C <worktree> branch --show-current)
gh pr list --head "$B" --state all --json number,state,mergedAt --jq '.[0]'

PR state for the worktree's branchClassificationMERGED (regardless of merge method)Inactive candidate — reclaimableOPENActive — not a candidateCLOSED unmerged, or no PRStale candidate — confirm with the user before reuse For a MERGED squashed branch, reuse means re-pointing the worktree at a fresh branch off the updated base ( rename-worktree) — do not rebase or merge the old branch forward, since its commits duplicate content the base already carries in squashed form.

Batch cleanup: scripts/prune_merged_worktrees.py automates this same gh pr list --head check (with a git-native merge-base --is-ancestor fallback when gh is unavailable) across every non-main worktree in a repository at once — use it instead of the manual per-worktree steps above when clearing out several stale worktrees. Defaults to --dry-run; pass --execute to actually remove eligible worktrees, -d/ --delete-branch to also delete the local branch, --scan <root> to sweep multiple repositories.

1. If an inactive worktree exists → reuse via the rename-worktree topic (rename the directory + metadata, switch branch)

2. If no inactive worktree exists or the user opts for new → git worktree add

New-commit-start trigger (HARD STOP — paired with git.md)#

When committing new work on a main/master/develop branch, if git status shows uncommitted changes from another task, worktree splitting is mandatory.

Entry conditions (any one)

• Current branch = main/master/develop
• git status shows 1+ changed files outside the new work (e.g., another task's unstaged files)
• Unpushed commits include another task's work

Decision tree on entry

text

git status (check for other changes)
  ├─ 0 other changes, branch = PR/feature → commit in place
  ├─ 0 other changes, branch = main/master/develop
  │    → AskUserQuestion: (a) create PR branch from current (b) create PR branch in a new worktree
  ├─ 1+ other changes, branch = main/master/develop
  │    → worktree split required. Leave other changes in place, isolate new work in a new worktree
  └─ Another task running on a PR branch with stray changes on main
       → Report to the user (confirm intent of stray changes) → decide worktree split + stray cleanup

Worktree split procedure

1. Leave the new work's diff in place — do NOT stash (preserve the working directory)
2. git -C <repo> worktree list to inspect inactive worktrees (per the decision tree above)
3. Inactive candidate present → reuse via rename-worktree; otherwise git -C <repo> worktree add .claude/worktrees/<branch> (or the worktree path defined by the active environment context — see worktree.md "Default Path Rules")
4. cd into the new worktree, then git checkout -b <new-branch> (or use the existing inactive branch)
5. Re-apply the same diff in the new worktree via Edit (the original main changes stay on main)
6. add → commit → push → PR inside the new worktree

Don't / Do

#Don'tDo1main has other changes; add the new file + commit + push anywayRun git status → if other changes exist → split into a worktree → commit in the new worktree2Hide other changes with git stash and commit on mainstash breaks the other task's intent/sequence. Worktree split is safer3Assume "my changes only — no conflict"Other working-directory changes can spill over (tests, builds, IDE state)4Omit "worktree split" from the AskUserQuestion commit optionsIf branch is main/master/develop and other changes exist, "split into worktree + create PR branch" must be the first option

Don't / Do#

#Don'tDo1Default to git worktree add <path> <branch> whenever a worktree is neededgit worktree list first → check inactive candidates → consider rename-worktree2"Temporary verification — create new and delete" pattern (wastes resources)Reuse a merged-PR worktree (e.g., one stuck at the merge commit) via rename3AskUserQuestion options offer only "create new worktree"Include "reuse an existing worktree by rename" whenever an inactive worktree exists4Decide on the worktree autonomously before asking the userWhen inactive candidates exist, ask which one to reuse5Ignore merged-PR worktreesReclaim them with move-worktree or rename-worktree6Place "create new worktree" as option 1/Recommended when inactive candidates exist****Reuse is Recommended/option 1. New is option 2 or below7"Unknown purpose for the inactive candidate → recommend safe new" thinkingInspect the inactive candidate state ( git log, git status) first. If still ambiguous, ask the user which to reuse — but keep reuse as option 1

Recommended placement rule (HARD STOP — prevent 2nd recurrence)#

When building AskUserQuestion options for worktree selection:

Inactive candidatesOption order + Recommended0Option 1: New worktree (Recommended). Option 2: Hold1Option 1: Reuse inactive by rename (Recommended). Option 2: New worktree. Option 3: Hold2+Option 1: Rename inactive A (Recommended). Option 2: Rename inactive B. Option 3: New worktree. Option 4: Hold

The Recommended marker must attach to the reuse option. "Safer to default to new because purpose is unclear" is an autonomous judgment — instead, document the "verify current commit/branch before reuse" procedure in the rename option description so the user can decide.

Self-check (before any worktree work)#

1. Did you call git -C <repo> worktree list?
2. Did you run the operation-state gate (Flow step 2) on every candidate? A worktree with CHERRY_PICK_HEAD/ MERGE_HEAD/ REBASE_HEAD or unmerged status codes (DU/UU/AA…) is mid-operation → excluded from candidates, no discard/stash options for its files
3. Does any gated worktree match (a) the same commit as HEAD or (b) a merge commit hash? → inactive candidate
4. If inactive candidates exist, include both the new-add option and the reuse option in AskUserQuestion
5. Is the Recommended marker attached to the reuse option? (apply the "Recommended placement rule" table)
6. Use new-add only when 0 inactive candidates exist OR the user explicitly chose new

Typical failure mode#

When a worktree is needed for plan verification, defaulting to "create new + remove later" wastes resources. git worktree list often shows merged-PR worktrees stuck on the merge commit hash — these are reuse candidates. Always inventory first before creating a new worktree.

Quick Reference#

ghq Clone (automatic SourceGit registration)#

When ghq get <url> is executed, the following happens automatically:

1. Clone the repository
2. Register in SourceGit (under the appropriate group)
3. Auto-create the group if it doesn't exist

Proceeds automatically without user confirmation

Detailed guide

SourceGit Management#

Directly edit the SourceGit GUI client's configuration file to add repositories, create workspaces, rename folders, etc.

Key features:

• Add/remove repositories
• Create workspaces
• Sync ghq repositories
• Update paths on folder rename

Detailed guide

ghq Migration (to-ghq) / Bare conversion (to-bare)#

• to-ghq (formerly migrate): bare+worktree → regular .git at the ghq path ( ~/ghq/host/group/repo/). Auto bare+worktree conversion, optional symlink, nested groups. Detailed guide
• to-bare (inverse): regular repo → bare + worktree at a custom location (e.g. .claude/worktrees/), preserving uncommitted changes. Includes a Windows lock pre-check (SourceGit/VS Code handle on .git blocks the rename). Detailed guide

Repo Patrol (batch inspection)#

Batch inspect and clean up the status of repositories under ghq.

Key features:

• Parallel collection of status, stash, unpushed for all repositories
• Status-based processing (commit-splitter integration, stash pop, push)
• Optional fetch all at the end

Detailed guide

Common Workflow#

1. Repository migration: Migrate to ghq structure with to-ghq topic (or to-bare for the inverse)
2. SourceGit update: Register new paths with sourcegit topic
3. Batch inspection: Clean up uncommitted/unpushed changes with patrol topic
4. Baseline .gitignore hygiene: Ensure standard ignore rules ( .worktrees/, .DS_Store, __pycache__/, *.bak, *.tmp) in .gitignore or .git/info/exclude to isolate worktrees and suppress runtime/editor clutter

Scripts#

• ./scripts/repo-to-ghq.sh - Move a repository to the ghq path (bare+worktree → regular)
• ./scripts/repo-to-bare-worktree.sh - Convert a regular repo → bare + worktree (inverse)
• skills/git-repo/scripts/local-to-staging-pr.sh - Cherry-pick local commit to a staging branch; prints manual push/PR commands by default, or pass --push [--body-file <path>] to also push and open the draft PR.
• skills/git-repo/scripts/prune_merged_worktrees.py - Detect and safely remove clean worktrees whose branches are already merged (GitHub PR lookup + git-native ancestry fallback); defaults to --dry-run. See the "Worktree decision tree" squash-merge caveat above.