repo-hygiene: clean-build.sh --apply accepts caches manifest entries without --include-caches (wrong-tier bypass)

[kyle-sexton]

Problem

clean-build.sh passes a fixed "build caches" allow-list to clean_apply_manifest on both apply paths (clean-build.sh lines ~95 and ~120), regardless of --include-caches. So clean-build.sh --apply --manifest <path> without --include-caches still accepts caches entries from a caller-supplied manifest and removes cache targets (.pytest_cache/, .ruff_cache/, …) even though the invocation selected the build-only tier. A stale or mistaken cache manifest thus bypasses the wrong-tier hardening that the ALLOWED-classes parameter exists to enforce.

Low severity (caches are regenerable, and it requires a caller-supplied/stale manifest), but it defeats the tier-isolation guard on the documented --manifest surface.

Fix direction

Derive the allowed classes from INCLUDE_CACHES: pass "build" when INCLUDE_CACHES=0 and "build caches" only when --include-caches is set, so a plain build apply accepts only build lines. Add a TDD case: a build-only --apply with a manifest containing a caches line must reject it (Rejected (wrong tier)) and leave the cache target in place.

Context

Surfaced by a Codex review comment on PR #1066 (Batch D), but the code lives in clean-build.sh (landed via #1023) — out of that PR's scope, so tracked here. Part of the repo-hygiene hardening umbrella #1003.

Work-class: C3 (bug-fix-shaped) — attended triage 2026-07-23, operator-ratified. 🤖

[kyle-sexton]

This was generated by AI on operator direction.

Superseded — this item was already ratified and should not have been queued.

The earlier first-drain ratification request on this issue was raised in error. The admission gate dispatches a C3 bug-fix-shaped item when it carries either its own recorded ratification or a completed first drain — and this issue already carried recorded ratification in its body from attended triage on 2026-07-23. The drain cycle applied the blanket first-drain rule without first reading bodies for an existing ratification, so it queued an item that was already admitted.

Restored to the autonomous frontier: agent-ready re-applied, needs-human removed. No human action is required, and this issue no longer appears in the attended queue's ratify view.

[kyle-sexton]

This was generated by AI during the work-loop admission gate.

Classification

• Work class: C3 scoped, bug-fix-shaped — clean-build.sh --apply accepts caches-manifest
  entries without requiring --include-caches, a wrong-tier bypass in existing gating logic.
  Bounded fix to existing code, not a new capability.
• Type: Bug (tracker's existing type).

Intended dispatch

Queued for the first-drain C3 ratification gate — first_drain_complete is still false, so
this bug-fix-shaped C3 candidate needs its own recorded ratification before dispatch. Ratify by
replying on this comment via /work-items:attend-queue, or it clears automatically once
first_drain_complete flips true.

[kyle-sexton]

This was generated by AI during the work-loop admission gate, on the operator's behalf.

Ratification

Operator ratified this item's C3 bug-fix-shaped classification and dispatch, direct in the
/work-items:work-loop session (standing autonomous-lane authorization, explicit "take on up to
5 items" instruction). Flipping to autonomous-eligible; re-entering the worker loop's frontier for
dispatch this cycle.