[ANT1OFF]

Why

The disk was nearly full and 66 Gram worktrees had piled up, mostly from finished, merged and archived workers. The sweep had already freed most of their node_modules, but it never removed them. Two causes showed up on a real machine:

Leftovers	Why the sweep kept them
~40 archived workers whose PR merged (e.g. #60, #61, #98, #99)	Once GitHub answers that an archived thread's PR merged, the publisher drops that thread's state. badgeFor then returns undefined, workerPrBadges gives [undefined], anyPrOpen reads the unknown PR as open, and mergedAndDone is false. So the 10-minute MERGED_GRACE_MS never applied, and every merged archived worker waited the 14-day removeAfterDays. All of the Gram 1.x leftovers were 7 days old or less.
~15 archived workers with no PR of their own (reviewers, research, release cuts on a detached HEAD)	remove needs hasPr, so these were only ever freed. A test named it a rule: "never removes a worker with no PR".

Not gaps, checked and left alone:

• local-checks is already pruned by local-checks.ts retention: passes are kept 30 days and other checks 7, logs are capped at 256 MB, and abandoned work folders are reclaimed after an hour. On this machine it was 57 MB with work/ empty.
• Worktrees from the 0.x app (gram-private) belong to another app's store. The 1.x sweep never knew about them.

What changes

• Archived merged workers: a parked thread completed on a merge (completedReason: "prMerged", completedAt set) that follows no extra PRs and has no badge still open counts as merged-done. It goes after MERGED_GRACE_MS. checkWorktree still asks GitHub about the bound PR afresh and needs it merged or closed, the worktree clean, and HEAD on a remote.
• Archived workers with no PR: a parked worker with no bound PR, no badge and no extra PRs gets remove a day (ARCHIVED_GRACE_MS) after its last activity, marked withoutPr. sweepStep removes it only when it's clean, HEAD is on a remote, and GitHub answered that no PR is open for its branch (noPrOpen). A failed lookup keeps it. Plain (non-worker) threads with no PR still aren't removed, and neither are unarchived workers.
• A process working in the worktree keeps it. Right before it frees node_modules or removes a worktree, the sweep lists every process's working folder: lsof -d cwd on macOS, /proc/*/cwd on Linux. If any is inside the worktree, it does nothing (inUse / freeUnlessInUse). If it can't tell (Windows, a failed scan), it also does nothing. Thread state alone can't see an agent still running after an archive, a dev server or an outside shell.
• The Settings › Storage toggle copy names the new rule.

Nothing else changed: removal still goes through closeAtRest, which refuses a dirty tree, a busy thread or a running terminal. Threads held by others, threads waiting on the user and orchestrators are still skipped, and no branch is ever deleted.

Independent review fixes (findings 1–5)

#	Finding	Fix	Refusal test
1	An adopted worker in a user-made worktree outside .worktrees got removed	Every thread, workers included, is swept only directly inside the repo's own .worktrees/	Adopted worker outside, merged worker elsewhere, nested folder and unknown repo are never due
2	status.showUntrackedFiles=no hid untracked files from the clean check and from git worktree remove	STRICT_STATUS_ARGS (--untracked-files=all --ignore-submodules=none --ignored=no) in the sweep, the Storage probe and worktreeCleanliness; git worktree remove runs with -c status.showUntrackedFiles=all	Real repo with the config set: the sweep reads it dirty, removeWorktreeDir refuses, the file survives
3	Pr.status returns undefined when gh isn't ready, which read as "no PR open"	No-PR removal needs gh pr list --state open itself to succeed and list none (by branch, or by commit when detached). Pr.status no longer feeds it	Signed out, missing, timed out, garbage or open PR: kept
4	Closing the thread deleted its pending wakes	A thread with a wake isn't removed (checked when judged and again right before the close); freeing still runs	No-PR and merged threads with a wake: removal not due
5	The grace counted from last activity, not from the archive	Thread.parkedAt, stamped by the store when an edit archives a thread and dropped on unarchive; grace counts from max(activity, parkedAt). Threads archived before this wait the full M days	Quiet 3 days, archived 1 h ago: not due. Store test for the stamp

Also from the review's lower-severity notes: a detached HEAD is kept under refs/gram/swept/<thread id> before its worktree goes (if that can't be written, the worktree stays), a free step scans processes once instead of twice, and the Storage copy is fixed. For each finding, putting the old line back makes its new test fail.

Verification

• At 1a656a2: bunx vitest run packages/contracts packages/git packages/server/src/git packages/server/src/persistence apps/web/src/settings: 179 files, 1935 passed, 16 skipped. lint, typecheck, fmt:check, check:scaffold pass.

• bunx vitest run packages/server/src/git/: 33 files, 326 passed, 13 skipped. worktree-gc.test.ts is 19/19.

• Live-process test: a real sleep runs inside a temp worktree's node_modules. The sweep's free step leaves every file in place, and frees the folder once the process exits. With the guard line taken out, this test fails.

• A worker in the same state as feat-voice-vocab (open, cold between turns, no PR, never completed) is asserted never due.

• bunx vitest run packages/server/src/git/ apps/web/src/settings: 76 files, 682 passed, 13 skipped

• The new tests run against the old worktree-gc.ts fail 6 of 15, including "removes an archived merged worker after the grace, though its badge was dropped". With the fix, 15/15 pass.

• bun run typecheck, bun run lint, bun run fmt, bun run check:scaffold pass.

• Full bun run check is left to CI and the merge gate. The machine is shared.

Known limits

• A reviewer worktree on a detached HEAD whose PR branch was deleted and pruned from the remote reads as unpushed and is kept. That's the safe side. It didn't happen on this machine, so it isn't handled here.
• Ignored files (e.g. .env.local, notes in ignored folders) aren't counted by any clean check and go with git worktree remove, as they already did for the close dialog and Storage cleanup.
• The process guard sees only processes whose working folder is inside the worktree, not ones holding files open there from elsewhere (an editor, a bun --cwd run). An idle thread's live agent session or a shell left at its prompt keeps its worktree until the session is evicted.
• Removal closes the thread. A branch it had stays, and a detached HEAD is kept under refs/gram/swept/. restore_worktree can't bring back a worktree that had no branch.
• On Windows the process guard can't tell, so the sweep acts on nothing there. No Windows releases are published.
• The process check, like the thread check, runs right before the step and isn't held across the deletion (the existing "known and accepted gap").
• Not live-qualified against a running app. Covered by unit tests and git-backed tests with a stubbed gh.