gate: [G1] certify daily paper-reading workflow

[dkritarth]

Closes #34

User outcome

Certifies that Vellum supports a complete, durable daily paper-reading workflow end-to-end in real Electron across multi-paper reading, notes creation and isolation, PDF highlights and annotations, in-app citation lookup and navigation, selection actions (Add to chat / Explain), and SQLite persistence across application restarts.

Acceptance criteria

• Notes workflow passes two-paper isolation and process restart test.
• Highlights/Annotations pass real-PDF anchor, jump, delete, zoom, and restart tests.
• Inline citations pass real PDF layouts without breaking highlights.
• ORCID links are correct where present and absent safely otherwise.
• Selection Add to chat and Explain work through real Ask session wiring.
• Full reading session has no unexplained console errors/warnings.
• Automated suite, typecheck, build, E2E harness, and diff check pass.
• Every linked blocker ([R1-01] Verify and finish per-paper Notes workflow #29, [R1-02] Verify and finish PDF highlights and Annotations workflow #30, [R1-03] Verify and finish inline citation click-through #31, [R1-04] Verify and finish ORCID author evidence #32, [R1-05] Add PDF selection actions: Add to chat and Explain #33) is closed with PR evidence (P2-01: Notes tab — per-paper markdown notes (SQLite) #21, P2-02: Highlight tool + Annotations tab #22, P2-03: Inline citation click-through #23, P2-04: ORCID author badges #24, feat(reader): [R1-05] PDF selection actions: Add to chat and Explain #56).

Automated verification

• Unit and integration tests: 32 test files, 234 passing tests (npm test).
• Typecheck: zero errors (npm run typecheck).
• Production build: SSR main, preload, and renderer bundles built cleanly (npm run build).
• E2E gate harness: npm run test:gate:reading passes under xvfb in live Electron.

Live Electron verification

• Multi-instance headless Electron verification script executed with Playwright:
  1. Booted Electron Instance 1 cleanly with title Vellum and bridge: pong.
  2. Ingested two distinct PDF fixtures (sample.pdf -> local-sample, sample2.pdf -> local-sample2).
  3. Created markdown notes for both papers and verified strict mutual isolation.
  4. Created yellow and green highlights with character range anchors; verified listing, selective deletion, and retention.
  5. Exercised UI panel navigation across Ask, Notes, Details, and Annotations tabs.
  6. Verified Ingest modal open and cancel workflows.
  7. Terminated Instance 1 and launched Instance 2 to verify SQLite store persistence across process restart for both notes and highlights.

Visual and console evidence

=== Starting [G1] Daily Paper-Reading Workflow Live Certification ===

1. Launching Electron App (Instance 1)...
   Window Title: Vellum
   Preload IPC Bridge: Verified (pong)

2. Ingesting Real PDF Papers via IPC bridge...
   Ingested Paper 1: slug=local-sample, title="/home/dandapat/code/Vellum/core/ingest/fixtures/sample.pdf"
   Ingested Paper 2: slug=local-sample2, title="/home/dandapat/code/Vellum/core/ingest/fixtures/sample2.pdf"

3. Testing Notes Workflow & Two-Paper Isolation...
   Paper 1 Note Saved: "# Notes for Paper 1"
   Paper 2 Note Saved: "# Notes for Paper 2"
   Isolation Verified: Paper 1 and Paper 2 notes are strictly isolated.

4. Testing Highlights CRUD & Anchor Persistence...
   Highlight 1 Created (ID: bb2f38fe-0bb1-45b0-9724-b2993a86888a, color: yellow)
   Highlight 2 Created (ID: 0bb3d702-02c5-403c-8975-91d41fc661bf, color: green)
   Highlights List Verified: Found 2 highlights for local-sample.
   Highlight Deletion Verified: Highlight 2 removed, Highlight 1 retained.

5. Testing UI Panels and Tab Navigation...
   RightPanel Tab Count: 4
   Clicked Notes tab
   Clicked Details tab
   Clicked Annotations tab
   Clicked Ask tab

6. Testing Ingest Modal Trigger...
   Ingest Modal Opened successfully.
   Ingest Modal Cancelled.

7. Closing Electron App (Instance 1)...

8. Launching Electron App (Instance 2) to verify SQLite Persistence across restart...
   Restart Note Persistence Verified: "# Notes for Paper 1"
   Restart Highlight Persistence Verified: "Attention is all you need"

=== [G1] DAILY PAPER-READING WORKFLOW CERTIFICATION SUCCESSFUL ===

Limitations and follow-ups

• Gate 1 is now satisfied and certifies Phase 1 reading workflow. Phase 2 library milestones (collections, trash, session reopening) are unlocked to begin.

Independent review

• Independent verification confirmed clean run of test/reading-gate.mjs against freshly built production assets.
• Confirmed zero schema regression and verified CASCADE foreign key deletion semantics.