278 — Worktree hygiene audit: archive before you prune

Date: 2026-10-15 PR: #2334 Story: story-issue-1487 / gh:#1487

Goalpost coming in

The Worktree Hygiene Protocol already said merge-time cleanup should be the default, with a periodic audit sweeping anything left behind. In practice the fleet still accumulated hundreds of stale dispatch/* worktrees — many merged by squash, many dirty only on project-docs/*, and a few still carrying unique unmerged design/blog drafts.

What shifted

This pass treated the audit classes as operational truth, with one correction: synlynk worktree audit must be run from the main checkout. Running it from a nested job worktree reclassifies main as a parent and floors nearly every nested worktree to needs-review, hiding hundreds of SAFE removals.

What shipped

1. synlynk worktree clean --apply from main removed 277 confirmed-SAFE worktrees/branches (merged ancestors, patch-equivalent, or stale registrations).
2. A second triage pass reclassified 162 additional NEEDS-REVIEW items as safe (committed state already on main / patch-equivalent / noise-only / superseded volatile forks) and removed them.
3. 55 unique files that were missing on origin/main were archived under docs/archive/worktree-hygiene-2026-10-15/ with a MANIFEST before their source branches are eligible for deletion.
4. Four open-PR worktrees were left untouched: #2241, #2175, #1970, #2264.

On the autonomy arc

Autonomous fleet operation needs a maintainer loop that can prune without discarding unique work. This audit is that loop executed once at scale, and it surfaces a follow-up: gh PR lookup via head:branch search is missing open PRs that gh pr view finds, so open work currently lands in NEEDS-REVIEW instead of UNSAFE.

New goalpost

Keep the four open-PR worktrees intact, land the archive PR, then escalate the remaining differs-only branches whose committed trees still diverge from main on non-volatile paths.