loadAgents merges <cwd>/agents/*.md on top of the extension's baseline:
a repo agent wins on name collision and may add brand-new agents. The
unknown-agent error now names both searched directories.
/pygienium-<check> is now resume-aware (terminal checks skipped unless
--fresh) and shares run-state with all/resume; every check gets a verify
hook that fails loudly when a sub-agent returns ok with no artifact;
run-state clears stale errors on retry success and reconciles a run as
failed only when every check failed. Drops the superseded
hygiene-state.ts model.
phases.ts becomes a live chat widget (spinner + tool-call tree) and the
check-runner posts per-agent tool-call summaries and an expandable
completion tree through a custom message renderer; footer.ts adds the
static pipeline-overview status strip for single checks and /pygienium-all.
All per-check artifacts, all-summary, and export move from pygienium/ to
.pygienium/; ensureRunStateIgnored appends .pygienium/ to the target
repo's .gitignore on first run (opt out with --no-gitignore), so a run
never stages its own output. Export now reads a single canonical root.
/pygienium-todos inventories TODO/FIXME/HACK markers and stub bodies via a
deterministic pre-scan plus the todos sub-agent; --fix converts silent
stubs (placeholder returns, empty/pass bodies) into loud failures,
never implementing TODOs or deleting markers. Replaces the noop
reference check; the extensibility suite now registers a synthetic
witness. Adds agents/todos.md and tests/todos.test.ts.
Single source of truth for what pygienium inspects (implementation-code
extensions, exclude dirs, .d.ts/.min.* exclusions) shared by recon,
dead-code, deep-modules, defensive-guards, comments, and complexity.
Every scan task and agent prompt injects the shared scope rules instead
of copy-pasted per-check lists.
