A GitHub repo link stranded at cloneStatus 'cloning' can never be re-cloned

[atomantic]

Problem

cloneRepoInBackground (server/services/brain.js) stamps cloneStatus: 'cloning' and only resets it from the promise callbacks of githubCloner.cloneRepo. If the server restarts (or is killed) while a clone is running, those callbacks never fire and the link record stays at cloning forever.

That state has no exit:

• POST /api/brain/links/:id/clone (server/routes/brainLinks.js:177-182) rejects with 409 CLONE_IN_PROGRESS whenever cloneStatus === 'cloning'.
• The Links tab only renders a Clone button for cloneStatus === 'none' and a Retry button for 'failed' — a cloning record gets neither (client/src/components/brain/tabs/LinksTab.jsx).

So the bookmark is permanently stuck showing a clone spinner with no way to retry short of editing the record by hand.

Fix

Give a stale cloning record a way back. Options, in order of preference:

1. Reconcile at boot. On server start, sweep links with cloneStatus === 'cloning' and reset them to failed with a cloneError explaining the interruption — no in-process clone can survive a restart, so any such record at boot is by definition orphaned. This alone restores the existing Retry affordance with no new UI or API.
2. Optionally, let the clone route force-restart a clone whose record has been cloning past a staleness threshold, instead of a blanket 409.

Note this is a record-state sweep, not an AI or network call, so it is fine to run at boot (no cold-bootstrap LLM concern).

Acceptance criteria

• After a server restart mid-clone, the affected link reports Clone failed with an explanatory cloneError and offers Retry.
• Retry actually starts a new clone (no 409).
• A test covers the boot-time reconcile: a record left at cloning is reset, and records in every other cloneStatus are untouched.

Related to #5442 — that issue bounded the client poll for a stuck clone (it now gives up after 10 minutes and labels the badge (stalled)), but deliberately left the stranded server-side record alone as out of scope.

[atomantic]

Local Codex review remained unsatisfied at its three-round cap, so this claim is stopping before a PR per the fail-closed review policy.

The local branch claim/issue-5463 contains the boot recovery, Retry coverage, peer-aware ownership work, and staged clone handling; the focused suite passes (245 tests). Remaining reviewer findings are: apply staleness uniformly to untagged mixed-version attempts; preserve and scope interruption cleanup provenance until cleanup succeeds; schedule post-grace staging cleanup; and move staging into a collision-free reserved namespace.

The assignee and in-progress marker remain in place for cold pickup.