[iLevyTate]

Stacked on #114. Base is fix/complete-phase-and-preview-ux; GitHub retargets this to main when #114 merges. The diff below is only this change.

Summary

Reproduced from a manual run's log: 8 files analyzing, 70 more added mid-run.

• 17:03:26 first batch completes → showAnalysisCompletionNotification schedules a jump to Organize in 2 s.
• 17:03:27 the 70 queued files start as the next run.
• ~17:03:28 the jump fires anyway (it only checked "still on Discover?"). Discover unmounts and its cleanup aborts the run: Analysis interrupted by navigation, main reports cancelled: true, processed: 0.
• 17:06:34 the user returns to Discover; resume restarts all 70. Because the run lived inside Discover, isAnalyzing locked every phase tab for the whole run (~43 s/file), so the first batch could not be reviewed or organized.

Changes:

• Auto-advance skips when another run is active or queued, checked when the timer fires (pendingFilesRef or store isAnalyzing).
• Run ownership: useAnalysis moves out of DiscoverPhase into a new AnalysisRunProvider mounted in PhaseRenderer around every phase, with the stuck-run watchdog and the total-failure flag. Discover reads it via useAnalysisRun(). A phase change no longer unmounts the run, and files queued mid-run survive leaving Discover.
• Navigation: a running analysis no longer pauses the phase tabs (NavigationBar.isBlockedByOperation), selectIsNavigationPaused (Alt+Arrow, dashboard links, File-menu pickers) or Discover's Continue (still needs ≥1 analyzed file). File moves, loading and undo/redo still pause. Switching to the dashboard still waits for the run, since the dashboard replaces PhaseRenderer.
• Merge guard: the run's final merge drops results for paths in the organized index, so a file organized mid-run is not re-added under its old path.

Scope

• Area(s): discover/analysis run, phase navigation, dashboard links
• Risk Level: medium (moves run ownership; navigation rules change)
• Breaking Changes: none; the behavior change is intended (tabs open during analysis)

Type of Change

• Bug fix
• Enhancement
• New feature
• Refactor
• Documentation update
• Breaking change

Test Plan

Automated

• npm run format:check / npm run lint (changed files; pre-commit hooks)
• npm test — full suite: 940 suites green after updating the 7 tests that encoded "analysis pauses navigation"
• npm run typecheck, npm run verify:checkjs-ratchet
• Additional tests added/updated when behavior changed
  • useAnalysis.test.js — auto-advance stays on Discover when the next run has started (confirmed failing with the fix disabled); moves to Organize otherwise
  • AnalysisRunProvider.test.js (new) — run survives a phase change, actions reach Discover, total-failure flag, missing-provider error
  • DiscoverPhase.test.js — Continue stays enabled during analysis once a file is ready
  • Updated: phaseNavigation, usePhaseJump, useKeyboardShortcuts.phaseGating, DashboardView, PhaseRenderer
• Full npm run ci / e2e not run locally

Manual QA

• Manual checklist completed (see docs/TESTING.md)
• Not applicable (explain below)

Manual QA notes (not yet run in the app):

1. Start a batch, add more files mid-run → when the first finishes, the app stays on Discover and the queued run starts (no interrupted by navigation in the log).
2. Go to Organize mid-run → the "Analysis continuing in background: N/M" banner keeps advancing; moving ready files works.
3. Return to Discover → the same run is still going, not restarted.
4. Dashboard toggle stays disabled until the run ends.

Checklist

• I scoped this PR to one logical change
• I self-reviewed code and naming for clarity
• I updated docs/config references where needed (comments describing run ownership)
• I called out follow-up work or known limitations

Known limitations

• The provider mounts with PhaseRenderer, so with a persisted isAnalyzing after a reload the resume now starts at app launch rather than when Discover opens.
• useAnalysis now loads in the PhaseRenderer chunk instead of the Discover chunk (still lazy, after the shell paints).
• Discover's embedding-rebuild prompt still only appears if Discover is open when a run ends.