Clean Worktrees (aka CW / prune-worktrees)

Sweep dead git worktrees out of the current repo. Agent isolation and the session-lock skill spin up worktrees under .claude/worktrees/<name>/ (or <repo>.worktrees/<name>/); after a PR merges or a session ends, the worktree lingers on disk with a merged or [gone] branch. This skill removes the dead ones safely and leaves everything live untouched.

This is the worktree counterpart to clean-branches (which sweeps branches). A worktree holds a branch checked out into its own directory, so the two are complementary: remove the dead worktree here, then clean-branches deletes the now-free branch (or this skill deletes it inline).

When this fires

  • “clean worktrees”, “cw”, “prune worktrees”, “prune-worktrees”
  • “clean dead worktrees”, “remove stale worktrees”, “tidy up worktrees”
  • “which worktrees can I delete?”
  • After a batch of PRs merge and the .claude/worktrees/ dir has grown.

What a worktree is (and why they pile up)

git worktree checks a branch out into a second working directory that shares the repo’s .git. Sources in this setup:

  • Agent isolation — the Agent tool’s isolation: "worktree" and the harness’s per-session worktrees (.claude/worktrees/<name>/). Auto-removed if unchanged, but a worktree that got any commit is left behind.
  • session-lock — ai-session.sh worktree <branch> isolates a top-level session into its own worktree.
  • Manual — git worktree add.

None of these self-clean once they have commits, so they accumulate.

Definitions

Category Criteria Action
Prunable stub Worktree record whose directory no longer exists on disk (removed manually) git worktree prune
Dead Linked worktree, clean tree, branch merged into origin/main OR upstream [gone] with no unique unpushed commits, no live session, not the current/main worktree git worktree remove + delete its branch
Dirty Uncommitted changes, or unique commits not on origin/main and not pushed Skip — flag; only --force after explicit confirmation
Active Live session-lock session registered, the current worktree, the main worktree, an open PR on its branch, or last commit < 7 days old and its PR has not merged Skip — never touch
Locked git worktree list marks it locked Skip unless the user confirms; then git worktree unlock before removing

“Clean tree” and “branch landed” must both hold for Dead — a clean tree whose commits never merged is Dirty (unpushed work), not dead.

Procedure

1. List worktrees

git worktree list --porcelain

Each block gives worktree <path>, HEAD <sha>, and branch <ref> (or detached / locked / bare). Note the main worktree (the repo root — dirname of git rev-parse --git-common-dir when .git is a directory) and the current worktree (git rev-parse --show-toplevel). Never remove either.

2. Prune admin stubs (safe)

git worktree prune only drops records for worktrees whose directory is already gone — it never deletes a directory. Preview, then prune:

git worktree prune --dry-run -v
git worktree prune -v

3. Classify each linked worktree

Refresh remote-tracking state once up front so the merged / [gone] checks below are accurate:

git fetch --prune origin

Then, for every worktree except the main and the current one:

a. Dirty check — uncommitted work

git -C <path> status --porcelain    # any output → DIRTY, skip (or --force only on confirmation)

b. Unpushed / unmerged check — unique work that lives nowhere else

git -C <path> rev-parse --abbrev-ref HEAD                 # the branch
gh pr list --head <branch> --state open --json number,url  # LIST_PRS — open PR? (glab mr list on GitLab)
git rev-list --count origin/main..<branch>                # commits ahead of main
git rev-list --count <branch>@{upstream}..<branch> 2>/dev/null \
  || echo "no-upstream"                                   # unpushed commits (or no remote)

Evaluate in this order so the label matches the Definitions table:

  1. Open PR → Active, skip (short-circuits — takes precedence even if the branch also has unpushed commits).
  2. Else ahead of main and (unpushed or no upstream) → Dirty (unpushed work), skip.
  3. Else ahead of main but fully pushed → Active, skip.

c. Branch-landed check — is the work safely on main?

# --format gives plain names — plain `git branch --merged` prefixes a branch
# checked out in a linked worktree with `+` (not two spaces), so a fixed-column
# grep would miss every branch this skill evaluates. -Fxq: fixed string + whole
# line, so a branch name with regex metachars (`.`, `+`, `*`) can't match loosely.
git branch --merged origin/main --format='%(refname:short)' \
  | grep -Fxq "<branch>" && echo MERGED
# -Fx: fixed string + whole line, so a branch name with regex metachars
# (`.`, `+`, `*`) can't match loosely. for-each-ref emits exactly "<branch> [gone]".
git for-each-ref --format='%(refname:short) %(upstream:track)' refs/heads \
  | grep -Fxq "<branch> [gone]" && echo GONE

Merged into origin/main, or upstream [gone] with no unique commits (3b returned 0) → the work has landed.

Squash-merge repos break both checks above — verify via PR state instead. A squash merge rewrites the branch’s commits into one new commit on main, so the branch’s own commits are never ancestors of origin/main: git branch --merged won’t show it as MERGED, and step 3b’s ahead-of-main count won’t be 0, so the [gone]-with-no-unique-commits path won’t fire either — both landed checks silently fail on every squash-merged branch, misclassifying it as Dirty (unpushed work) instead of Dead. Don’t trust local ancestry for landed detection in a squash-merge repo (check git log --oneline -5 origin/main for single-commit messages — GitHub’s default squash-commit subject is "<title> (#N)", though a repo can configure a different template (e.g. Lacaedemon/sparta uses "PR #N: ...") — or just try it, the false positive is cheap to spot once you know to look). Use the PR’s own merge state as the authoritative signal instead:

gh pr list --head <branch> --state all --json number,state,mergedAt --jq '.[0]'

A "state": "MERGED" entry means landed regardless of what the ahead/merged checks above say. (Hit on Lacaedemon/sparta, 2026-07-02: ~40 of 48 worktrees slated for cleanup showed ahead=2 to ahead=15 on the naive check — every one had actually merged via squash minutes to hours earlier.)

A detached worktree has no branch, so the squash-merge escape hatch above does not apply to it — and the naive check it falls back to is the one that is wrong in a squash-merge repo. Every landed-detection route in 3b and 3c keys on a branch name: gh pr list --head <branch>, git branch --merged, <branch>@{upstream}. A detached HEAD answers none of them, so classification silently drops to the ahead-of-main count — which the warning above already establishes is meaningless here, since a squash merge guarantees it is nonzero.

The result reads as the safe answer while being the wrong one. ahead=5 with no branch and no upstream looks exactly like commits that exist nowhere else, so the worktree is labelled Dirty and kept indefinitely, when in fact its work merged hours earlier.

Diff the content instead, which needs no branch:

h=$(git -C <path> rev-parse HEAD)
git diff --name-only origin/main "$h" -- <files the unique commits touched>

Scope it to those files. A bare git diff origin/main <head> reports every file main has gained since the worktree was cut, which in an active repo is hundreds — all of it main’s drift rather than the worktree’s work, and it buries the answer. Get the file list from the worktree’s own commits first, then diff only those:

git log --name-only --format='' "origin/main..$h" | sort -u

Note the $h rather than HEAD. A detached worktree’s head is not the head of wherever you are running the command, so a bare HEAD silently reports on the current checkout instead — and without --name-only --format='' the command prints commit messages rather than the file names the next step needs. An empty diff means the content is on main and the worktree is Dead.

(2026-07-29, the same ai-config sweep: two detached worktrees showed ahead=5 and ahead=2 and were classified Dirty on that basis. Narrowed to the files their own commits touched, both diffed empty against main — one was PR #804’s review fixes, already squash-merged, and the other’s two commits were both present in jules-review.yml on main. The whole-tree diff for the same pair reported 222 and 221 changed files, which is why the narrowing matters.)

d. Live-session check — is another session using it?

# Plain `list` (NOT `--all`) — it prunes stale records and shows only LIVE
# sessions, so a worktree whose session already died won't be flagged Active.
~/.claude/skills/session-lock/scripts/ai-session.sh list 2>/dev/null \
  | grep -F "<path>"        # a live record on this worktree → ACTIVE, skip

(If session-lock isn’t installed, skip this check — fall back to the dirty and recency guards.)

e. Recency check — too fresh to judge

git -C <path> log -1 --format='%ci'    # last commit < 7 days → Active, skip

A worktree is Dead when 3a is clean, 3c says landed, 3d finds no live session, and 3e is older than 7 days.

A merged PR overrides the recency guard: a branch whose PR merged can go however recent it is, provided it carries no unpushed work. The guard exists to protect work that is still in progress, and a merged PR is the definitive statement that it is not. Holding a worktree for six more days on the strength of a date, when its own PR closed hours ago, is the guard firing on the one case it was never written for — and it is the common case in an active session, where the worktrees most worth sweeping are the ones created that week.

So the age check only decides worktrees whose landed status is unknown. Once 3c has answered, age adds nothing.

Verify the no-unpushed-work half rather than assuming it from the merge. The natural check — does origin/<branch> still exist — answers a different question in a repo that deletes head branches on merge, since every merged branch reports remote=GONE there. That is equally consistent with “merged and cleaned up” and with “merged, then you committed something else locally”, and only the second is unsafe.

Compare the branch tip’s date against the PR’s mergedAt:

tip=$(git log -1 --format='%ct' "<branch>")                          # epoch seconds
merged=$(gh pr view <N> --json mergedAt --jq '.mergedAt|fromdateiso8601')   # VIEW_PR
[[ "$tip" -lt "$merged" ]] && echo "OK (tip predates merge)" || echo "tip AFTER merge -- inspect"

Compare epochs, not the ISO strings. %cI renders the commit’s date in the machine’s local zone while mergedAt is UTC, so a lexicographic < between them compares clock faces from two different zones. It fails in the unsafe direction: west of UTC, a tip committed after the merge still sorts first, reports OK, and the worktree gets removed with that commit on it. Verified with tip=2026-07-30T18:00:00-07:00 against merged=2026-07-30T23:00:00Z — the tip is two hours later in real time and the string comparison says it predates. %ct and fromdateiso8601 put both on the same absolute scale, and fromdateiso8601 is available in the jq that gh --jq embeds.

A tip predating the merge cannot carry anything the merge did not see. A tip after it is the case worth stopping for, and it is the same orphaned commit that CLAUDE.md’s merge-race note describes — work pushed onto a branch whose PR had already closed.

  • Do: treat a merged PR plus a tip predating its merge as Dead, whatever the age.
  • Do: compare timestamps, since remote=GONE is uninformative wherever head branches are auto-deleted.
  • Don’t: skip a worktree for recency alone once its PR has merged.
  • Don’t: read a deleted remote branch as proof nothing local was added after the merge.

(2026-07-29, an ai-config sweep: four worktrees, all clean, all four remotes gone, and PRs #625/#643/#782/#810 all merged. Two were 1 and 2 days old, so the recency guard alone would have kept them. Every tip predated its own merge by 7 to 14 hours, and the maintainer’s standing rule is that branches from merged PRs can go unless they have unpushed work.)

4. Present the plan (dry run) — wait for confirmation

## Worktree Cleanup Plan — <timestamp>

| Worktree | Branch | Status | Action |
|----------|--------|--------|--------|
| `.claude/worktrees/loving-bhabha-1051e7` | `ums-…-clobber` | Dead (PR #56 merged, clean) | 🗑️ Remove + delete branch |
| `.claude/worktrees/pedantic-shamir-b52cab` | `claude/pedantic-…` | Active (open PR) | ⏭️ Skip |
| `.claude/worktrees/tender-feistel-5c7311` | `claude/tender-…` | Current worktree | ⏭️ Skip |
| `(stub) old-scratch` | — | Prunable (dir gone) | 🧹 Pruned in step 2 |

Proceed? (or pick specific worktrees)

No silent removals. Wait for confirmation; “just go” / “do it” → proceed with all proposed removals.

5. Remove dead worktrees

git worktree remove <path>          # refuses on a dirty tree — a safety net; do NOT blindly --force
git branch -d <branch>              # -d refuses unless merged; the work landed, so this should pass

If git worktree remove reports the tree is dirty, that worktree was misclassified — re-inspect, don’t reach for --force. Only --force after the user explicitly OKs discarding that worktree’s changes.

Exception — a worktree containing a submodule: the error fatal: working trees containing submodules cannot be moved or removed is a different refusal, triggered by the submodule’s presence alone, not by dirty state. If git -C <path> status --short is empty (genuinely clean), --force here is correct and safe — it isn’t the dirty-tree case above, so don’t treat it as a misclassification signal.

If git branch -d refuses (squash/rebase merge can hide the merge), confirm the PR merged (gh pr list --head <branch> --state merged) before git branch -D.

A branch that was ever pushed as a PR head is recoverable after deletion, so a -D here is far less consequential than it looks: GitHub retains refs/pull/N/head permanently, and it still resolves once the branch is gone (git fetch origin refs/pull/<N>/head). See memories/git.md, “GitHub keeps refs/pull/N/head forever”. The exception is the one that matters — a branch never pushed has no such ref, which is why an unpushed worktree branch still needs confirmation.

A squash merge does not reliably force that refusal, so expect both outcomes in one sweep. git-branch(1) checks the branch against its upstream — “fully merged in its upstream branch, or in HEAD if no upstream was set”. So a branch still tracking a live origin/<name> passes -d regardless of what main contains, printing warning: deleting branch 'X' that has been merged to 'refs/remotes/origin/X', but not yet merged to HEAD. Only once the remote ref is gone (auto-delete on merge, or gh pr merge --delete-branch) does the check fall back to HEAD and refuse. A sweep of 29 branches split 18 -d / 11 -D on that basis alone. So don’t read a needed -D as a red flag, and don’t read a successful -d as proof the work reached main — step 3’s classification is what establishes that, not the deletion flag.

6. Final prune + report

git worktree prune -v               # clears any record left by the removals
## Worktree Cleanup Complete — <timestamp>

### Removed (dead)
- `.claude/worktrees/loving-bhabha-1051e7` (branch `ums-…-clobber` deleted; PR #56 merged)

### Pruned stubs (dir already gone)
- `old-scratch`

### Skipped (active / current / fresh)
- `.claude/worktrees/pedantic-shamir-b52cab` — open PR
- `.claude/worktrees/tender-feistel-5c7311` — current worktree

### Flagged — dirty / unpushed (left alone)
- `.claude/worktrees/wip-experiment` — 2 uncommitted files; your call

Safety rules

  • Never remove the main working tree (git worktree remove refuses anyway).
  • Never remove the current worktree — the one you’re running in (git rev-parse --show-toplevel).
  • Never --force a dirty worktree without explicit confirmation — uncommitted or unpushed work exists nowhere else.
  • Never remove a worktree with a live session-lock session — another agent is working there.
  • Always present the plan first — no silent removals.
  • Don’t remove worktrees newer than 7 days — likely in-progress work. Unless the branch’s PR has merged and its tip predates that merge, in which case age is irrelevant (step 3e).
  • git worktree prune is safe (records only, never directories) — but still report what it pruned.

Relationship to other skills

  • session-lock / deconflict-sessions — creates the worktrees this skill cleans up; consult its registry (step 3d) so you never remove one a live session holds. Its own teardown is git worktree remove at session end; this skill is the bulk sweep for the ones that slipped through.
  • clean-branches / cb / prune — the branch counterpart. Run it after this skill (or let step 5 delete branches inline) so a removed worktree’s branch doesn’t linger. Same dry-run-then-confirm discipline.
  • clean-git — the combined sweep. It runs this skill and then clean-branches, behind one dry-run plan and one confirmation, and owns the ordering constraint that makes worktrees-first mandatory.
  • post-merge — after a PR merges, removing its worktree is part of the tidy-up (step 2 there); that skill can hand off here for a repo-wide sweep.
  • wrap-up — the session-level bookend surfaces leftover worktrees and offers to run this skill to sweep the dead ones.

Anti-patterns

  • ❌ git worktree remove --force on a dirty tree to “just clean it up” — silently destroys uncommitted work.
  • ❌ Removing a worktree whose branch has unique unpushed commits (work lives only there).
  • ❌ Removing a worktree another session-lock session is actively using.
  • ❌ Removing worktrees without a dry-run plan and confirmation.
  • ❌ Deleting the branch but leaving the worktree (or vice versa) — sweep both.
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