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.
