initial import: @mikefreno/omp-pygenium (omp port)

tasks/12-orchestrator-all.md

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+# 12. /pygienium-all master orchestrator
+
+meta:
+  id: pygienium-12
+  feature: pygienium
+  priority: P2
+  depends_on: [pygienium-07, pygienium-08, pygienium-09, pygienium-10, pygienium-11]
+  tags: [orchestration]
+
+objective:
+
+- Implement `/pygienium-all`: run every registered check in sequence as ordered phases under a unified status strip, with resumable state and a final summary report.
+
+deliverables:
+
+- `src/modes/all.ts`: `runAllChecks(opts)` iterating the registry, calling `runCheck` per check with shared recon, accumulating per-check status into run-state, writing `pygienium/all-summary.md`
+- `/pygienium-all` command wired in index.ts with phase strip listing all check names
+- Respects `--fresh`, `--fix`, and `--only=comments,complexity` to select a subset
+
+steps:
+
+- Implement `runAllChecks`: init a single run (mode "all"), run shared recon once, then for each registered check call `runCheck` with the existing run-state record (not a fresh one per check)
+- Build the phase strip from registry names; set initial phase to the first check
+- Aggregate final summary: per-check status, artifact paths, total findings/changes counts
+- Support `--only` filtering via the command-target parser
+
+tests:
+
+- Integration: run `/pygienium-all` on a small repo; assert every check ran, run-state shows all complete, all-summary.md present
+
+acceptance_criteria:
+
+- `/pygienium-all` runs every registered check exactly once in registry order
+- Interrupted runs are resumable (in_progress/failed checks re-run; complete ones skipped unless `--fresh`)
+- all-summary.md lists per-check outcomes
+
+validation:
+
+- Inspect `pygienium/run-state.json` and `pygienium/all-summary.md`
+
+notes:
+
+- This is the piolium "balanced"/"deep" mode analogue, but simpler: one run, sequential phases, shared recon
+- Ensure scheduler is not needed (sequential) unless we later parallelize independent checks