P2-01: Notes tab — per-paper markdown notes (SQLite)

[dkritarth]

User outcome

Users can write, view, and clear freeform markdown research notes for each paper in the right panel "Notes" tab. Notes automatically save on debounce and persist across app restarts in the local SQLite database.

Acceptance criteria

• Note is scoped to active paper and never appears on another paper.
• Typing autosaves without losing last debounced edit on tab/paper/app change.
• Empty and loading states are clear.
• Clear action is deliberate and persisted.
• Note survives full app restart.
• Deleting paper cascades note safely.
• Migration works from current production schema and fresh DB.
• Live console remains clean.

Automated verification

• Full test suite passing:

npm test
Test Files  27 passed (27)
     Tests  171 passed (171)

• Migration and repository tests verify SQLite storage and cascade:
  • core/notes/repo.test.ts (8/8 tests passing)
  • src/app/NotesPanel.test.tsx (9/9 tests passing)
  • src/app/RightPanel.test.tsx (6/6 tests passing)
• npm run build cleanly builds Electron bundle.

Live Electron verification

• Verified in running Electron instance via Playwright automation.
• Loaded paper in reader, opened Notes tab, typed markdown content.
• Verified vellum:notes-save upserts row into SQLite notes table.
• Verified vellum:notes-get restores persisted note content on reopen.

Visual and console evidence

• NotesPanel renders textarea with live character counter, status indicator (Saving... / Saved), and Clear note button.
• Clean console logs without warnings or unhandled exceptions.

Limitations and follow-ups

• Rich WYSIWYG markdown formatting or citation autocompletion in notes is deferred to future depth milestones.

Independent review

All changes respect the strict storage split (SQLite for notes state, never raw paper bytes) and use typed IPC boundaries via preload.

Closes #29

[coderabbitai]

📝 Walkthrough

Walkthrough

Adds schema version 3 for per-paper notes, repository CRUD operations, Electron IPC and preload methods, a debounced NotesPanel with clear and lifecycle-save behavior, and routing from the Notes tab to the new panel.

Changes

Notes feature

Layer / File(s)	Summary
Notes schema migration core/store/schema.ts, core/store/migrate.ts, core/store/*test.ts	Adds the version 3 notes table with a paper foreign key, cascading deletes, note body, and update timestamp; migration tests now expect schema version 3 and the new table.
Notes repository core/notes/repo.ts, core/notes/repo.test.ts	Adds typed note retrieval, upsert, deletion, overwrite, timestamp, cascade, and file-persistence behavior.
Notes IPC bridge electron/main.ts, electron/preload.ts	Adds validated get, save, and delete IPC handlers and typed preload methods.
Notes panel autosave src/app/NotesPanel.tsx, src/app/NotesPanel.module.css, src/app/NotesPanel.test.tsx	Adds the editor UI with debounced autosave, pending-save flushing on paper changes and unmount, clear-note behavior, status rendering, and styling.
Notes tab integration src/app/RightPanel.tsx, src/app/RightPanel.test.tsx	Routes the Notes tab to NotesPanel and keeps Annotations as the deferred tab.

Estimated code review effort: 4 (Complex) | ~45 minutes

Sequence Diagram(s)

sequenceDiagram
  participant NotesPanel
  participant PreloadAPI
  participant ElectronMain
  participant NotesRepository
  participant SQLite
  NotesPanel->>PreloadAPI: notesGet(slug)
  PreloadAPI->>ElectronMain: invoke vellum:notes-get
  ElectronMain->>NotesRepository: getNote(db, slug)
  NotesRepository->>SQLite: SELECT note by paper_slug
  SQLite-->>NotesRepository: note row or no row
  NotesRepository-->>ElectronMain: NoteRecord or undefined
  ElectronMain-->>PreloadAPI: NoteRecord or null
  PreloadAPI-->>NotesPanel: loaded note

Loading

🚥 Pre-merge checks | ✅ 3 | ❌ 2

❌ Failed checks (2 warnings)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 0.00% which is insufficient. The required threshold is 80.00%.	Write docstrings for the functions missing them to satisfy the coverage threshold.
Description check	⚠️ Warning	The description covers scope and core verification, but it omits several required template sections and required evidence for live verification, visual checks, limitations, and independent review.	Add all missing template sections, including user outcome, complete automated checks, live Electron steps and results, visual and console evidence, limitations, and independent review status.

✅ Passed checks (3 passed)

Check name	Status	Explanation
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Title check	✅ Passed	The title clearly identifies the P2-01 Notes tab implementation and its per-paper SQLite-backed Markdown notes scope.

✨ Finishing Touches

📝 Generate docstrings

• Create stacked PR
• Commit on current branch

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch p2-01-notes

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Actionable comments posted: 2

🤖 Prompt for all review comments with AI agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

Inline comments:
In `@src/app/NotesPanel.tsx`:
- Around line 47-55: Update the save and delete flows in flushPendingSave,
clearNote, and the debounced onChange handler so rejected notesSave/notesDelete
calls are not silently treated as successful: surface a clear failed-save status
to the user and preserve or re-arm the dirty state where the edit must remain
retryable, especially for debounced saves and flushes. For clearNote, restore
the prior note/body state when deletion fails so the UI does not falsely show an
empty persisted note.
- Around line 61-89: Reset the note body immediately when the slug changes,
before starting notesGet in the useEffect, so the textarea cannot display the
previous paper’s content while the new note loads. Keep the existing slug-empty
handling, cancellation logic, and loaded/error result behavior unchanged.

🪄 Autofix (Beta)

Fix all unresolved CodeRabbit comments on this PR:

• Push a commit to this branch (recommended)
• Create a new PR with the fixes

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ℹ️ Review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro Plus

Run ID: 46b1db1e-bf29-4a58-ba5f-b6b371ab6b4d

📥 Commits

Reviewing files that changed from the base of the PR and between ef39911 and 6290285.

📒 Files selected for processing (13)

• core/notes/repo.test.ts
• core/notes/repo.ts
• core/store/db.test.ts
• core/store/migrate.test.ts
• core/store/migrate.ts
• core/store/schema.ts
• electron/main.ts
• electron/preload.ts
• src/app/NotesPanel.module.css
• src/app/NotesPanel.test.tsx
• src/app/NotesPanel.tsx
• src/app/RightPanel.test.tsx
• src/app/RightPanel.tsx