Audit agent skills against authoring best practices + bump openspec to 1.3.1 - #309

Audit pass against Anthropic's skill authoring guide
(platform.claude.com/docs/en/agents-and-tools/agent-skills/best-practices).

Skill content
- Rename `galahad` → `quality-checks`. The "galahad" name is opaque
  unless you know Jonathan Lange's principle by name; the guide
  flags vague names as an anti-pattern. Body still credits the
  Galahad Principle as the source.
- Rewrite `quality-checks` description with explicit trigger
  phrases (`# type: ignore`, `# noqa`, `as any`, `@ts-ignore`,
  `# pragma: no cover`, "skip/quarantine a test") so discovery
  matches the authoring guide's "what + when" recommendation.
- Surface `code-ratchets`' bundled `ratchet.py` and
  `.pre-commit-config.yaml` at the top of SKILL.md so Claude copies
  the shipped files instead of regenerating equivalents from the
  inline snippets.
- Split `madsci-cli` (440 → 278 lines) and `madsci-managers`
  (425 → 302 lines) using the guide's progressive-disclosure
  pattern: SKILL.md becomes a navigation index pointing at
  `reference/*.md` files for the long catalogs (command reference,
  template manifest format, per-manager notes, db handler details).

Engine
- `_copy_skills` now copies every file in a skill directory rather
  than only `SKILL.md`, so reference files and bundled scripts
  propagate to projects generated from `lab/`, `module/`,
  `workflow/`, and `experiment/` templates. Per-skill copy logic
  extracted to `_copy_skill_directory` to keep within the existing
  C901 complexity budget.

Tests
- Update `test_template_engine.py` skill assertions to count
  non-skill files structurally instead of pinning hardcoded totals
  that broke when skills started shipping multiple files.
- Strengthen `test_bundled_skills_match_repo_skills` to walk the
  full skill directory tree rather than comparing only `SKILL.md`.
- Add `test_skill_reference_files_copied` regression test for the
  multi-file copy path.
- 312/312 tests pass; ruff clean.

Lockfile / docs
- `skills.lock.json`: rename `installName` to `quality-checks`. The
  `digest` field is now stale until the next sync against the
  upstream `luckierdodge/skills` rename, which has already landed
  on that repo's `main`.
- `docs/guides/agent_skills.md`: refresh the skill listing for the
  rename and clarify what `quality-checks` enforces.

…json

The two repo-level skills (`quality-checks`, `code-ratchets`) are now
plain vendored files under `.agents/skills/` and `.claude/skills/`.
Removing the lockfile avoids the stale `skillPath: skills/galahad`
pointer and the digest-drift footgun on the next sync — we don't need
to track these as managed dependencies on a personal upstream.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>