Cleanup Project

Get a repository to a clean foundation before new work: every uncommitted change decided, ignore files updated, merged branches deleted locally and on origin, and an up-to-date, clean main.

When to use

• "Clean up this repo before I start the next feature."
• "Delete the branches that are already merged, local and remote."
• "My working tree is a mess. Help me decide what to keep and get back to main."
• "Tidy the .gitignore and get rid of stale branches."
• "Is spike/llm-cache worth keeping?" This goes straight to the single-branch drill-down (Step 6).

Don't use it to remove dead code or unused imports (code-review mode:cleanup), commit and push everything (auto-push), cut a release or tag (ship), or add LICENSE, CONTRIBUTING and other OSS files (oss-ready). For a git how-to question ("branch -d vs -D?"), answer it directly and run no workflow.

Inputs

• Base branch. main by default. If the repo has no main, ask once which branch is the base (master, develop, trunk) and use that answer everywhere this skill says main.
• Remote. origin by default. If git remote lists no origin, ask once: use another remote (by name), or run local-only. Use that answer everywhere this skill says origin. Local-only means no fetch, no pull, no push, and no remote delete; the report says local-only.
• Scope. Infer it from the request, then confirm it once in one line (Scope: sweep (Steps 1, 3, 5, 6, 7). OK?).

Scope	Example request	Steps
full (default)	"clean up this repo before the next feature"	1–7
review	"help me decide what to keep in my working tree"	1, 2, 3, 7
ignore	"fix the .gitignore"	1, 3, 4, 7
sweep	"delete the merged branches"	1, 3, 5, 6, 7
report-only	"which branches are merged? don't touch anything"	1, Step 5 up to the table, Step 6 list
drill-down	"is spike/x worth keeping?"	1, then Step 6 drill-down for that branch

Step 1 always runs. Steps 3 and 7 run in every scope except report-only and drill-down. Report-only never switches, pulls, discards, or deletes. Residue left by a phase outside the scope is reported — skipped by user and does not make the run PARTIAL. Per-scope details: references/scopes-and-results.md.

Prerequisites

Check these before Step 1. If one fails, stop and print the report as BLOCKED — <failed check>.

• git rev-parse --git-dir succeeds (inside a git repository).
• The base branch resolves: git rev-parse --verify main or origin/main, or a confirmed base.
• No operation is in progress: git rev-parse -q --verify fails for MERGE_HEAD, REBASE_HEAD, CHERRY_PICK_HEAD and REVERT_HEAD, and test -d "$(git rev-parse --git-path rebase-merge)" fails, as does the same for rebase-apply (never test a literal .git/... path: in a linked worktree .git is a file). Never "clean" through a conflict.

Repo Sync Before Edits (mandatory)

This skill syncs first, but not with the usual stash → pull → pop:

git fetch origin --prune        # refresh refs; the working tree is untouched

Do not stash or pull before Step 2: a stash hides the state the user must review, and a pull into a dirty tree can conflict before anything is decided. The pull happens in Step 3. If the fetch fails, show the error and ask once: continue local-only, or stop (BLOCKED — fetch failed). With no origin, the Inputs answer applies instead.

Rules for every destructive step

1. List → explicit confirm → execute. Show the exact commands with real names. A "no", or silence, means nothing runs.
2. If the user confirms only part of a list ("yes except feat/x"), re-show the edited list and take a fresh yes.
3. If a command fails, stop that plan and report the error. Never retry with force or a stronger flag (-D for -d, --force, --ignore-other-worktrees).
4. Protected branches are never deleted, renamed, or force-pushed: main, master, develop, trunk, release/*, the current branch, and any branch in a branch refs/heads/<b> line of git worktree list --porcelain. If the user asks to delete one, refuse and name the rule. For a worktree branch, tell them to run git worktree remove <path> first.

Workflow

1. Fetch and snapshot

1. Run the sync above.
2. Record the current branch (or detached HEAD), base, git status --porcelain=v1 -z, and git worktree list --porcelain. If main is checked out in another worktree and Step 3 is in scope, warn now that the run will stop BLOCKED at Step 3, before any Step 2 plan is confirmed.
3. Run gh auth status. It decides whether the merged-PR signal is available (not a stop condition).
4. If HEAD is detached, run git log HEAD --not --branches --remotes --oneline. If it prints commits, report them and offer git switch -c <name> to keep them (in report-only and drill-down, report them only).

2. Review each uncommitted change

1. Parse git status --porcelain=v1 -z (NUL-separated, so paths with spaces and both paths of a rename survive).
2. If there are more than 20 entries, show a grouped summary (by directory and status) and offer one decision per group. Show full diffs on request. You may propose groups; never infer a decision from them.
3. Show each entry with its status code and diff. If the path is secret-like (.env*, *.pem, *.key, *.p12, id_rsa*, credentials*), show only its name and size, never its content or diff, and print ⚠ secret-like: <path>.
4. Ask: keep (commit to wip/cleanup-<date>) / keep on disk + ignore / stash / leave as is / discard. Offer keep on disk + ignore only for an untracked path and only when Step 4 is in scope; it defers the path to Step 4. For a secret-like or local-config path, the offered default is keep on disk + ignore when that option is offered, and leave as is otherwise. Never default-commit a secret-like path.
5. After every entry has been asked, list the entries still without an answer and ask once: "leave these untouched?". Only an explicit leave or skip makes an entry undecided.
6. Show the consolidated plan (references/action-plans.md B) and take one yes. Nothing runs before that yes.
7. On yes, run the discards first: git restore --staged --worktree -- <path> (tracked), or git clean -n -- <path> then git clean -f -- <path> (untracked), with each path single-quoted and git --literal-pathspecs. Run -f only if the dry run names exactly the decided paths; otherwise stop and report. Never run bare git clean -fd.
8. Then commit the kept paths: git switch -c wip/cleanup-<date>, git add -- <kept>, git commit -m "<msg>" -- <kept> (the pathspec keeps other staged entries out); then run any stash. Commit on main only if the user explicitly asks.

Commands per status code, the stash form and the large-tree format: references/uncommitted-review.md.

3. Switch to an up-to-date main

1. Check git worktree list --porcelain. If a branch refs/heads/main line belongs to another worktree, stop and print the report as BLOCKED — main checked out at <path>; run /cleanup-project there.
2. If HEAD is detached, re-run git log HEAD --not --branches --remotes --oneline. If it still prints N commits and the user declined a branch, require the explicit answer "abandon these N commits" before switching. Without it, stop: BLOCKED — N commits on no branch.
3. Run git switch main. If git refuses because a change would be overwritten, name the path and ask once: commit it to the wip branch, stash it, or discard it. If it stays undecided, stop: BLOCKED — main not reached: <path> undecided. Do not loop back to Step 2.
4. Run git pull --ff-only. If it refuses because local main diverged, show git log --oneline origin/main...main and ask: continue without the pull, or stop (BLOCKED — main diverged). Never reset or force.
5. Run git rev-list --count origin/main..main and record N ahead of origin/main. Commits only on local main never qualify a remote ref as merged in Step 5.

4. Update the ignore files

1. Collect evidence: untracked artifacts and keep on disk + ignore paths from Step 2 (or from the Step 1 snapshot when Step 2 is out of scope; every untracked non-artifact path then counts as kept), plus tracked files that already match a rule (git ls-files -ci --exclude-standard).
2. Test the proposed patterns against every kept path (committed, stashed, or left as is): write them to a temp file and run git -c core.excludesFile=<tmp> check-ignore --no-index -v -- <kept paths>. If one matches, narrow or drop the pattern. keep on disk + ignore paths are exempt.
3. For each secret-like path, print ⚠ secret-like: <path> above the diff. If it is tracked, add that ignoring does not remove it from history and the secret should be rotated.
4. Show the full .gitignore diff and ask to apply it.
5. If approved, apply it and re-run git status --porcelain. Expect every covered path to be gone. If one remains, show git check-ignore -v -- <path> and fix the pattern.
6. Ask Commit on main? [yes / branch+PR / no] and follow references/action-plans.md C (its untrack variant for approved git rm --cached -- <p> paths: no pathspec on the commit). Pushing main, or pushing the PR branch and opening the PR, each needs its own yes. Branch+PR ends with git switch main; it and a declined commit make the result PARTIAL.
7. If a deferred path is not covered by a pattern applied on main, ask commit to wip / stash / leave as is / discard for it here (references/ignore-patterns.md). After branch+PR, report those paths under ignore rule pending in PR #N instead. Steps 2 and 3 do not repeat.

Candidate patterns and the tracked-but-ignored flow: references/ignore-patterns.md.

5. Sweep merged branches (local and origin)

Build candidates from local branches and origin/*, excluding origin/HEAD, origin/main and protected branches. Test a local <b> against main and origin/<b> against origin/main (see references/merged-detection.md). A branch is merged if any signal holds:

1. Ancestry: git merge-base --is-ancestor <b> main (or git branch --merged main).
2. Patch equivalence: git cherry main <b> prints only - lines, or the squash-tree check (a temporary commit of the branch tree on its merge-base) prints -.
3. Merged PR: gh pr list --head <b> --state merged returns a PR with base main whose headRefOid equals the branch tip. A tip that moved after the merge means unmerged new work.

Signals 2 and 3 are the squash evidence. If gh is unusable or any gh pr list call fails (including a non-GitHub remote), signal 3 is unavailable for the run: record it under Unverified: and continue with signals 1 and 2. This is not a Rule 3 stop and not PARTIAL.

1. Show the full candidate table (references/action-plans.md A). A new candidate found later needs its own confirmation.
2. In report-only scope, list a merged current branch as current, not deletable, then stop and go to the Step 6 list.
3. Take one explicit confirmation for the whole table.
4. Each side is deleted only on its own signal (local <b> vs main, origin/<b> vs origin/main); a side without one goes to Step 6. Locally, run git branch -d <b> when ancestry holds, or git branch -D <b> only with squash evidence (-d refuses those).
5. For a proven origin/<b>, run git push --force-with-lease=refs/heads/<b>:<sha> origin :refs/heads/<b>, where <sha> is the recorded tip. If origin/<b> moved, git rejects it as stale info: report the row as skipped with that reason.
6. Run git fetch origin --prune.

6. Report unmerged branches

1. List the unmerged branches with ahead/behind counts and last commit date. Do not delete them.
2. In report-only scope, offer only the read-only overview (never a plan from action-plans.md D), then print the report.
3. In every other scope, offer the per-branch drill-down. For a branch the user picks, build the overview from references/overview-fields.md.
4. Ask Delete / Archive / Open PR / Keep, then follow the matching plan in references/action-plans.md D.
5. In drill-down scope, skip items 1 and 2. If the named branch is merged, show its signal and offer the Step 5 delete for that one row. Otherwise run items 3 and 4 for it.

7. Verify the end state

git branch --show-current                 # expect: main
git status --porcelain                    # expect: empty
git branch --merged main                  # expect: only main and protected branches
git branch -r --merged origin/main        # expect: only origin/main, origin/HEAD and protected branches

1. Run the four checks. If one prints something else, report × <check>: <observed>; the result is then not PASS. If that leftover comes from a phase outside the scope, report it — skipped by user instead; it does not affect the result.
2. For each branch deleted locally whose remote delete was skipped, re-run the merge signals (ancestry, then squash evidence) on origin/<b> against origin/main. Report re-check origin/<b>: still merged (<signal>) or re-check origin/<b>: not merged. A ref that still qualifies needs a new table row and a new confirmation; one that does not is listed as remote kept — unproven.
3. If main is ahead of origin/main, report N ahead of origin/main. Ask to push only if the user did not already decline it in Step 4; otherwise name it under Next:.
4. Print the final report.

Results

Each result applies to the steps in scope (references/scopes-and-results.md).

• PASS, for the checks in scope: on main, git status --porcelain empty, and no unprotected merged branch left locally or on origin. main ahead of origin with the push declined is allowed and named under Next:.
• PARTIAL — reason: residue remains. Residue is anything that keeps the end state from PASS inside the scope: something the user chose (a stash, a change left as is, a declined discard, table row or ignore commit, an unmerged ignore PR) or a skipped or stale info delete. Name each item with its reason; join several with ; .
• BLOCKED — stop point: the run stopped at a prerequisite, at Step 3, or on an error.

A step with nothing to do reports √ pass (none needed).

Step Completion Reports

After each step, emit a short ◆ Cleanup (step N of 7 — <name>) block with one line per check: √ pass (<evidence>), × fail (<reason>), or — skipped by user. The template and the check names per step are in references/scopes-and-results.md.

Expected output

After the per-step blocks, a run ends with a final report that opens with the result:

◆ Cleanup Report
Result:      PASS
Verified:    show-current → main; status --porcelain → empty; branch --merged main → main;
             branch -r --merged origin/main → origin/HEAD, origin/main; 0 ahead of origin/main
Unverified:  none (merged-PR check available)
Next:        No approval needed
··································································
  Scope:              full
  Branch:             main (0 ahead of origin/main)
  Changes reviewed:   5 (1 kept → wip/cleanup-2026-10-05, 2 discarded, 2 ignored/deferred, 0 left as is)
  Ignore file:        +2 patterns, committed on main and pushed
  Merged deleted:     feat/login (ancestry, 1a2b3c4); feat/filters (squash-tree, 5d6e7f8);
                      fix/readme remote (merged PR #57, 9a0b1c2)
  Skipped deletes:    none
  Unmerged kept:      feat/search-v2, spike/llm-cache, wip/cleanup-2026-10-05
  Protected skipped:  release/2.1

Field rules (Unverified: and Next: values): references/scopes-and-results.md. A full worked run: references/example-output.md.

Acceptance Criteria

A run is correct when all of these hold:

• git fetch origin --prune ran before any ref was read; nothing was stashed before Step 2.
• Every uncommitted change in scope got an explicit decision; no secret-like content was printed or committed by default.
• The ignore diff was shown before it was applied; no kept path was ignored.
• Every deleted branch had recorded merge evidence; -D was used only with squash evidence.
• Destructive steps followed the rules above; protected branches were never deleted.
• The run ended on main with git status --porcelain empty and no unprotected merged branch left locally or on origin, or it reported PARTIAL or BLOCKED with the reason.

The report must also be understandable:

• The first line after the header gives PASS, PARTIAL or BLOCKED and the reason.
• Verified: (checks run and their output) is separate from Unverified:.
• Each deleted ref names its signal and its sha or PR number.
• Next: names the remaining user action or says No approval needed.

These are instruction checks. Without reviewer feedback, human understanding of the report stays unconfirmed; agent inspection cannot confirm it.

Edge Cases

• Local-only branch. No remote delete; the table shows local.
• Archive with differing tips. See references/action-plans.md D before the lease delete.
• User declines everything. Change nothing and print the report as PARTIAL.

Notes

• Context budget. In the drill-down, if git diff --shortstat main...<b> reports more than 1000 changed lines, summarize the diff with a subagent instead of reading it into the main context (references/overview-fields.md).