fix(hooks): preserve script-style hooks in the index; warn when nothing merges - #63
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…ng merges The ## Hooks index section filtered to .json fragments, so hooks directories using the pre-SPEC-004 script convention (.sh files) had their entries silently erased from AGENTS.md on every regeneration — files that exist on disk must never disappear from the index. - index now lists EVERY non-hidden hooks file: .json fragments are annotated 'merged into .claude/settings.json', anything else as a companion file (not merged; reference it from a fragment) - sync now warns when hooks/ contains only non-JSON files: they are indexed and synced but will never merge into settings.json, with the fragment shape to wrap them shown inline Fixes the acme AGENTS.md regression (backfill-session-id.sh / sync-permissions.sh dropped from the index). Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
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Fixes the regression Nick hit in the acme repo:
.agents/hooks/backfill-session-id.shandsync-permissions.shwere erased from AGENTS.md on index regeneration.Root cause
The SPEC-004 hooks bucket models hooks as
.jsonsettings-fragments, and the## Hooksindex section filtered to.json— so any hooks directory using the older script convention (.shfiles) lost its entries every timeindexran. The files themselves were never touched; only their index entries were destroyed. The merge engine already skipped non-JSON files harmlessly.Fix (both halves of the ask)
hooks/—.jsonfragments annotated "merged into.claude/settings.json", everything else annotated "companion file (not merged; reference it from a fragment)". Files on disk can no longer vanish from AGENTS.md.syncnow warns whenhooks/contains only non-JSON files — they're indexed and synced but nothing will ever merge into settings.json — and shows the exact fragment shape to wrap a script so Claude actually runs it.Tests
Two regressions reproducing the acme scenario exactly:
.sh+.jsonmix survives two index cycles byte-identically with correct annotations; script-only dir merges nothing, warns, and conjures no settings.json. Full suite green (go + all bats).To restore the acme index: re-run
sync-agents indexthere once this ships — the Hooks section comes back with both scripts listed.🤖 Generated with Claude Code