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85c54e7e78
Closes #181, closes #182, closes #183, closes #184, closes #185, and the residual half of #173. #185 — every per-surface check read ONE root, so a monorepo with `skills/` plus `plugins/*/skills/` scored only the first: 4 skills over budget, 2 reported, exit 0. The default now NAMES the bundles it did not score; `--bundles=all` scores them in one pass with one exit code. Root-only stays the default so a vendored third-party corpus is not scored as if it were yours. #181 — `orphan-docs` had a documented severity nothing read, and the duplicate-rules check had no id at all, so neither could be tiered. Both are real rules now and the exit code respects their severity. #183 — the log and `--json` disagreed (21 lines against 88 findings) because some checks print per finding and others per group. One computed total, printed and carried in `--json`. #182 — `--json-out=<file>` writes the JSON while stdout stays human-readable, so a CI job stops scanning twice. #184 — `vigiles test` resolves a harness's bare `vigiles` import from the CLI's own install, so `npx vigiles@<version> test` needs nothing in the project. NODE_PATH was measured, not assumed: Node ignores it for ESM. #173 residual — `lint` verified the integrity HASH, which says nothing about whether the things a file NAMES still exist, so an artifact committed while its refs were live stayed green after the target was deleted. The new `spec-refs` rule re-derives them. It immediately found four dead references in this repo's own `examples/CLAUDE.md.spec.ts`, left behind by the hexagonal refactor. BREAKING CHANGE: `orphan-docs` and `duplicate-rules` now default to "warn" — a repo relying on either to fail CI must set "error" explicitly. Registering them surfaced that both are heuristic proxies, and this repo's calibration rule is that a heuristic never defaults to error. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>