Stabilize track1 RC regressions for packs upmerge

[julianknutsen]

Summary

This PR packages the RC-gate stabilization work needed before merging back into codex/integration-track1-upmerge. It addresses the checked-in failure buckets from Actions run 24362910139.

1. Command discovery and docs drift

• Suppress startup pack/import command-collision warnings during normal CLI startup so JSON, tutorial, and acceptance output stays parseable.
• Fix broken local links under docs/packv2.
• Add regression coverage around the command discovery path.

2. V2 agent scaffolding expectations

• Update stale gc agent add acceptance coverage and txtar fixtures to current v2 city behavior.
• Align expectations with pack.toml + agents/<name>/ scaffolding instead of legacy city.toml mutation.

3. macOS rig/workdir path normalization

• Normalize rig and workdir path comparisons so macOS alias paths such as /var vs /private/var do not break hook and rig resolution.
• Add focused coverage for the normalized path behavior.

4. Workflow pool and retry recovery

• Reopen pool-routed work when its assigned session bead disappears.
• Preserve attached executable root types for retry attempts instead of coercing them into issue_type=molecule.
• Fix pooled retry recovery so a claimed attempt can be reclaimed and completed after a worker crash.
• Add unit and integration coverage around the reclaim path.

5. Integration harness and fixture alignment

• Fix the integration helper quoting bug that produced invalid TOML in reconciler tests.
• Update review-check fixtures to include gc.attempt where the current check scripts require it.
• Make the filebdshim ready path use real ready filtering so session beads are excluded.
• Update graph-dispatch harness assertions to match the current cleanup-and-reclaim trace sequence.

Breaking changes / migration notes

• No breaking changes in product behavior.
• Acceptance coverage was updated to reflect the current v2 gc agent add contract rather than the removed legacy behavior.

Testing

• make check
  Ran: make check
• make check-docs if docs, navigation, or links changed
  Ran: make check-docs
• make test-integration if runtime, controller, or workflow behavior changed
  I did not run the full make test-integration target. I reran the failing workflow/controller buckets directly:

Additional targeted verification:

• go test ./cmd/gc -run 'TestAddDiscoveredCommandsToRoot|TestTutorial01|TestRigAnywhere_RigFromCwdDir|TestCmdHookUsesAgentCityAndRigRoot|TestCmdHookPoolInstanceUsesTemplatePoolLabel|TestRigAnywhere_ResolveContext|TestRigAnywhere_ResolveRigToContext' -count=1
• go test ./internal/workdir -run 'TestConfiguredRigNameMatchesSymlinkAliasPath' -count=1
• go test ./test/docsync -count=1
• go test -tags acceptance_a -timeout 5m ./test/acceptance -run 'TestAgentAddCommands|TestAgentSuspendResume|TestConvergeCommands/List_JSON_ReturnsArray|TestSessionEmptyCity/List_JSON|TestStatusTutorialCity/JSON_ReturnsValidJSON|TestFormulaCommands/Show_GastownFormula_DisplaysSteps|TestOrderGastownCity/Show_DisplaysDetails' -count=1
• go test ./internal/molecule ./test/integration/filebdshim -count=1
• go test -tags integration ./test/integration -run 'TestRetryManagedPooledWorkerRecoversClaimedAttemptAfterCrash' -count=1 -timeout 12m -v
• go test -tags integration ./test/integration -run 'TestGraphWorkflowSuccessPath|TestGraphWorkflowFailureRunsCleanup|TestAdoptPRFormulaCompileAndRun|TestPersonalWorkFormulaCompileAndRun|TestRetryManagedPooledWorkerRecoversClaimedAttemptAfterCrash' -count=1 -timeout 30m -v

Checklist

• Linked an issue, or explained why one is not needed
  Tracked in bd as ga-7wbjg3.
• Added or updated tests for behavior changes
• Updated docs for user-facing changes
• Called out breaking changes or migration notes