feat: highlight, annotate, and copy passages as agent-ready changelist (#5)

[JohnnyBonk]

Implements the highlight + annotate + agent-export workflow from #5, plus a small unrelated UX change for the sidebar.

Summary

• Select markdown text → choose a colour or annotate with a note.
• Click an existing highlight → recolour, edit the note, copy, or delete.
• Right-side panel groups highlights by colour, with per-list and per-item copy in agent-ready format.
• Highlights persist per file in app_data_dir/highlights.json.
• Sidebar folders now default to collapsed.

Scope

Highlights — capture

• Selection popover with five colour swatches (yellow / orange / pink / blue / purple) plus Annotate and Copy.
• Number keys 1–5 apply the matching colour while the popover is open.
• Annotate swaps the popover row to an inline note input; Enter / Save creates the highlight in the active colour with the note attached.
• Active colour is persistent for the session; ] / [ cycle it without opening the popover.
• Code blocks are not highlightable in v1 (selection inside <pre> hides the popover).
• Welcome tab supports highlights via a synthetic :welcome storage key.

Highlights — re-engage

• Click an existing highlight → edit popover anchored to the span: current colour, recolour swatches, note display + edit, Copy, Delete.
• Delete / Backspace deletes the targeted highlight while the popover is open or the cursor is inside one.
• Inline checkmark flash on Copy and Delete buttons; bottom-right toast for global confirmation; Undo action (5s) on every delete path.

Review panel

• Toggle from the toolbar (highlighter icon, with an active-colour pip).
• Filter pills per colour with counts; "Copy all" / "Copy <colour>" in the header.
• Per-item note display and edit (pencil icon, hover-revealed).
• Click an item → scrolls the document highlight into view.

Agent-ready export format

Single item:

Source: /abs/path/to/README.md

> the selected passage
Section: Installation
Timestamp: 2026-04-29T10:43:12Z
Note: optional annotation

Whole list (per-list Copy) groups by colour:

Source: /abs/path/to/README.md

## List: pink

> uncited claim
Section: Performance benchmarks
Timestamp: 2026-04-29T10:44:27Z

Anchoring

Highlights store (sourceStartLine, sourceEndLine, passage, occurrenceIndex), leveraging the data-source-map attributes markdown-it already emits on block-level tokens. Re-applied as wrapping spans on every render, so they survive Shiki / Mermaid replacement passes. If a passage cannot be relocated after an upstream edit, the highlight is silently skipped (orphaned). Scroll position is saved and restored around the re-application pass to prevent browser scroll-anchoring from snapping to the top when the wrapper used as the anchor is removed during delete.

Persistence

• Single highlights.json under app_data_dir, keyed by absolute file path.
• Schema is forward-compatible: the note field uses serde(default, skip_serializing_if) so older files load cleanly and unannotated highlights stay compact.
• Two new Tauri commands: load_highlights and save_highlights_for_file.

Sidebar folders default to collapsed

Per-folder expansion state defaults to collapsed; the sidebar opens quietly each session and the user expands what they want. Repo-group headers (when grouping by repo) still default open so the outline stays visible.

Tests

• 27 Vitest cases covering anchoring, occurrence counting, agent-export formatting (with and without notes), and per-colour grouping.
• 7 Rust tests covering round-trip, missing/corrupt file fallback, camelCase JSON keys for the frontend, legacy file (without note) loads cleanly, and note omitted from JSON when unset.
• pnpm typecheck and pnpm build clean.
• Pre-existing failures in src/lib/markdown.test.ts and src/lib/theme.test.tsx also fail on main and are unrelated to this change.

Deferred (for follow-ups)

• Per-list description ("rules that apply to every item in the list").
• Renameable colour → list label.
• Pipe-to-agent integration.
• Multi-block selections (current implementation anchors to the start block).
• Snap-to-word selection.
• JSON / markdown-blockquote export format toggles.
• Sidecar JSON option (current store is global to app_data_dir).
• Edit history per highlight.
• Orphan UI for highlights whose passage can no longer be located.

Test plan

• pnpm install (the repo currently imports markdown-it-front-matter; this branch has it in the lockfile).
• pnpm tauri dev, open a markdown file with multiple paragraphs and headings.
• Click the highlighter button in the toolbar to open the panel.
• Select a passage; popover appears below the selection. Apply a colour via swatch or 1–5.
• Click Annotate, type a note, press Enter; highlight is created with the note.
• Click an existing highlight; edit popover appears. Recolour with a swatch, edit the note, then Copy. Confirm checkmark flash + toast.
• Click Delete on the popover; confirm inline "Deleted" flash + bottom-right Undo toast. Click Undo within 5s; highlight returns.
• With cursor inside a highlight, press Delete; same flow.
• Press ] and [ to cycle the active colour.
• In the panel, click a colour pill to filter, then "Copy" the visible list. Paste to verify format.
• Try selecting inside a fenced code block; popover should not appear.
• Reload Marky; highlights persist (~/Library/Application Support/marky/highlights.json on macOS).
• Edit the source file (typo elsewhere in the doc); existing highlights still appear.
• Sidebar: folders should be collapsed on first launch; expand state is per-session.