fix: correct stale skill exclusion text and mutation state display

[karngyan]

Claim

Two honesty bugs found in today's hands-on audit, plus a batch-abort regression the fix itself would have introduced:

1. Installed SKILL.md contradicted itself. Every generated package exclusion said "Do not block execution; this candidate is advisory until replay and shadow evaluation pass." — but mutations install only runs after replay and shadow both passed, and the same file states so two lines later.
2. mutations propose/synthesize printed a stale state column. Rows rendered the registration outcome's initial state, so a mutation that was already shadow_passed or retired displayed as candidate.
3. Template evolution must not abort re-proposal. Deterministic generation re-derives the same mutation id from the same evidence, so the new template phrasing conflicts with immutable packages registered under the old phrasing; the registry's refusal previously became a hard error that killed the whole propose/synthesize batch on any pre-existing database (reproduced against a real 69k-event corpus).

Fix

• autophagy-mutations: new candidates carry stage-neutral phrasing — "Do not block execution; this instruction is advisory." (ADVISORY_EXCLUSION); old text preserved as LEGACY_ADVISORY_UNTIL_REPLAY_EXCLUSION for structural matching.
• autophagy-install: stored packages are immutable and never rewritten; at render time the installer exact-matches the one legacy template line and renders the corrected text, leaving every other exclusion verbatim.
• autophagy-cli + autophagy-store: after registration, propose/synthesize fetch each generated mutation's current stored state and print that; a per-candidate MutationContentConflict becomes a warning ("earlier-template content; the stored immutable package is kept") instead of a batch abort. JSON note: reports gain an additive current_states map and (proposal, only when non-empty) a warnings array — no existing fields changed.

Evidence

• generated_skill_has_no_self_contradicting_exclusion and installer_tolerates_legacy_advisory_exclusion_phrasing (autophagy-install)
• generated_exclusions_stay_true_at_every_lifecycle_stage (autophagy-mutations)
• propose_and_synthesize_display_current_mutation_state_not_stale_candidate and propose_and_synthesize_survive_immutable_template_conflicts (autophagy-cli integration)
• Verified against a real-data copy: installing a legacy-phrased package renders the corrected SKILL.md section; re-running synthesize on a pre-existing registry warns twice and exits 0 with correct per-mutation states (active, candidate).
• mise run check green (exit 0, unpiped).

Privacy

None — template text and display state only; no new persisted data beyond the derived state map in command output.

🤖 Generated with Claude Code

https://claude.ai/code/session_015LY7xtercMc3NtLeX2z4YV