REGISTRY.a2ml drift recurs and blocks every PR — needs a regen step or pre-commit hook

[hyperpolymath]

Problem

The required check "Registry + topology in sync" (scripts/build-registry.sh --check) fails whenever .machine_readable/REGISTRY.a2ml source_hashes drift from the file tree — which happens any time a spec file changes without someone running just registry. Because it is a required status check, the stale registry then blocks every open PR, not just the one that caused the drift.

Observed

• 2026-06-11: PR perf(hypatia-scan): cache built scanner keyed on Hypatia HEAD + shallow clone #380 (an unrelated perf change) was blocked by this; the last 3 main commits also failed the check. Root cause: REGISTRY.a2ml source_hashes were stale (no structural change — just un-regenerated hashes).
• Fixed in-band by running just registry and committing the resync (rode in on perf(hypatia-scan): cache built scanner keyed on Hypatia HEAD + shallow clone #380), but the recurrence is unaddressed.

Proposed fix (pick one)

1. Pre-commit hook that runs just registry (or registry-check) and fails/auto-stages if REGISTRY.a2ml/TOPOLOGY.md drift — catches it at commit time.
2. CI auto-regen: a governance job that runs just registry and commits the result (bot) when drift is detected, instead of just failing.
3. At minimum, document in CONTRIBUTING that any .machine_readable/** change must be followed by just registry.

Filed during the 2026-06-11 estate review/cleanup pass.