fix(skills): sync repaired full skill content

[anotherben]

Summary

Sync the repaired full-skill content back into claude-harness so the repo matches the local no-shim skill surfaces.

Changes:

• update harness-update to sync full skill directories across Claude, Codex, Agents, Continue, Cursor, and the shared platform catalog
• make normal full-skill sync canonical with --delete, while preserving only explicitly local overlays marked as .local/, local.*, or *.local.*
• keep shim replacement as full-directory replacement from the shared platform source
• make the harness-update no-shim verification block self-contained when run in a fresh shell
• restore current-semantics plan-360-audit eval coverage
• preserve local safety guidance for deploy, vault, session heartbeat, and skills-index routing, including executable migration-directory checks
• sync the repo-local skills-index runtime support for task_bootstrap, routing bundles, candidate validation, and the daemon/proxy surface used by the updated vault skills
• harden skills-index freshness, external mirror target safety, daemon shutdown, and portable default path behavior

Regression check

• cd skills-index && npm ci && npm test — 28/28 tests passing
• cd skills-index && node --check src/cli.js && node --check src/daemon.js && node --check src/indexer.js && node --check src/store.js
• python3 -m json.tool skills/plan-360-audit/evals/evals.json
• python3 ~/.codex/skills/.system/skill-creator/scripts/quick_validate.py skills/deploy-checklist
• python3 ~/.codex/skills/.system/skill-creator/scripts/quick_validate.py skills/harness-update
• python3 ~/.codex/skills/.system/skill-creator/scripts/quick_validate.py skills/session-heartbeat
• python3 ~/.codex/skills/.system/skill-creator/scripts/quick_validate.py skills/vault-init
• python3 ~/.codex/skills/.system/skill-creator/scripts/quick_validate.py skills/vault-process
• python3 ~/.codex/skills/.system/skill-creator/scripts/quick_validate.py skills/plan-360-audit
• repo shim scan returned 0
• local-overlay smoke passed in both zsh and bash: evals/local.json survived and an unmarked removed-script.sh was deleted
• fresh-shell no-shim verification scanned all configured local roots and blocked on a seeded shim
• MIGRATION_DIR=. bash -c ': "${MIGRATION_DIR:?Set MIGRATION_DIR to your repo migration directory}"; ls "$MIGRATION_DIR"/ >/dev/null'
• MIGRATION_DIR=. zsh -c ': "${MIGRATION_DIR:?Set MIGRATION_DIR to your repo migration directory}"; ls "$MIGRATION_DIR"/ >/dev/null'
• local sync proof: all six local skill homes match the repo for the repaired skill dirs; all six local roots have 0 shim-only skills
• rebuilt skills-index via /Users/ben/.claude-harness/skills-index; status reports stale: false
• git diff origin/main...HEAD --check
• local pre-commit CodeRabbit-style review hook verdict: PASS

Blast radius

Limited to skill documentation/content, one eval JSON under skills/, and the repo-local skills-index MCP runtime/tests needed to expose the task_bootstrap contract referenced by the updated vault skills. No installer shell, package manifests, hooks, or generated database files are changed.

Edge cases

• explicitly marked local-only full-skill overlays survive normal harness sync
• unmarked destination-only files are deleted so removed upstream runtime assets cannot stay active
• no-shim verification does not depend on shell state from an earlier fenced block
• source SKILL.md transfer is verified, not just preservation of pre-existing files
• migration listing uses MIGRATION_DIR instead of an angle-bracket placeholder
• /run-verification remains user-invocable; the accidental local metadata hiding it was removed during local sync and is not part of this repo diff
• workspace/template folders without SKILL.md are skipped
• fresh repo-local installs expose the task_bootstrap tool instead of relying on this machine's global proxy
• sync-external --target is restricted to the managed platformRoot/external-skills tree and refresh deletes only the managed mirror repo child
• new skill files, routing registry edits, and external source manifest edits mark the compiled skills index stale
• daemon shutdown destroys connected client sockets before awaiting server close
• skipEmbeddings overrides globally enabled embeddings for daemon/quick-start paths
• upgraded compiled roots missing skill-routing.json rebuild instead of reusing stale old-shape artifacts

Conversations addressed

• Replaces local shim surfaces with full skill directories.
• Preserves repaired local full-skill value rather than downgrading to upstream-only copies.
• Syncs the repaired local full skills back into the source repo.
• Keeps the repo-local skills-index support in step with the local full skills that call it.

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