Fix Oracle selection packaging and mutation ingress stalls

[provencher]

Summary

Fixes two related reliability failures in MCP/Agent workflows:

1. Oracle / selection packaging

   • prevents deferred UI snapshots from overwriting newer canonical MCP selection
   • makes Context Builder discovery use the same canonical, per-tool-call selection persistence as ordinary Agent Mode
   • removes discovery-only selection roles, private revisions/CAS, and terminal selection publication
   • preserves newer canonical selection during terminal tab/UI application

2. Mutation ingress / file-edit stalls

   • decouples applied ingress from retained derived codemap convergence
   • uses immediate path-local authority revocation for create/edit/delete/move
   • fixes retained root/path fence ordering and actor hot-spin starvation
   • makes freshness timeout cancellation-independent so blocked work returns an error instead of dropping MCP transport
   • reduces clean manifest publication from repeated full-store scans to a single reusable scan path
   • returns correlated applied/fresh mutation acknowledgements

Closes #515
Closes #390

Architecture

The final selection design intentionally avoids Context Builder-specific authority. Successful selection-changing tool calls commit canonical state immediately, and later discovery failure does not roll those writes back. Context Builder keeps only genuine lifecycle/routing behavior (run binding, frozen worktree/review context, tool policy, final prompt/meta publication).

Validation

• Native architecture second opinion: no production blocker; direct Oracle packaging and terminal-race regressions added
• ContextBuilderSelectionTransactionTests: 6/6
• ContextBuilderWorkspaceContextTests: 12/12
• ContextBuilderNestedMCPFailureTests: 2/2
• ContextBuilderWorktreeInheritanceTests: 5/5
• TabContextRoutingTests: 47/47
• MCPMutationRetryableFailureTests: 13/13
• CodemapAutomaticSelectionBasicTests: pass
• CodemapStoreMutationTests: 3/3
• CodeMapRootManifestStoreTests: 28/28
• WorkspaceCodemapLocalGitClassificationTests: 10/10 plus repeated load-sensitive exact runs
• non-cooperative freshness-timeout regression: pass
• SwiftFormat/SwiftLint strict: pass
• swift build --product RepoPrompt: pass after rebase
• guardrails and commit/push secret scans: pass
• live rpce-cli-debug Agent selection/Oracle smoke: PASS (2 total / 2 full; Oracle read RepoPromptCE and MCPFileToolProvider)
• live mutation repro no longer drops transport; it now settles through the bounded tool contract under pathological loaded-workspace pressure

Two full root-suite attempts were run. The first exposed and led to hardening the Git-layout readiness budget. The second passed that boundary and failed only an untouched durable-artifact quarantine test, which then passed twice focused (0.023s each).

Notes

Rebased onto current origin/main. Main already contains the debug provenance JSON validator fix, so this PR carries no temporary packaging workaround.