feat(storage): PDF editor persists to per-file sidecar

Phase 2 (core swap). The PDF editor and split-view scratchpad stop
writing SQLite and persist to a per-file sidecar
`<pdfPath>.badnote.json` (debounced, atomic temp+rename+.bak) — so
annotations travel with the file. The source path is the identity
(no more djb2 doc-id).

- SidecarRepository wraps the Phase-1 store with debounced autosave.
- pen_editor: per-page ink, scratch-links AND highlights now persist
  to the sidecar and restore on reopen (closes persist-highlights).
- New "un-highlight" tool: tap a stored highlight to remove it — the
  highlight could not be removed before.
- split_view: each anchor's scratchpad lives in the sidecar's
  scratchLinks[id].scratchpad, keyed by anchor id.

Note: pre-existing SQLite annotations are migrated later (Phase 5);
note/slide editors swap in Phase 4. analyze clean, tests green.

lib/editor/canvas/pen_editor_screen.dart

@@ -16,9 +16,11 @@
 //      "highlight selection" action turns the current selection into stored
 //      normalized highlight rects.
 //
-// Persistence (strokes) reuses the existing EditorRepository / SaveScheduler
-// wiring verbatim. Highlights are in-memory only for now — see
-// TODO(persist-highlights).
+// Persistence (Phase 2): strokes, highlights and scratch-links all write to a
+// per-file SIDECAR (`<pdfPath>.badnote.json`) via SidecarRepository — debounced,
+// atomic (temp+rename+.bak). The source file PATH is the identity (the sidecar
+// IS the identity; the old djb2 path-hash document id is gone). Highlights now
+// survive reopen, and a stored highlight can be removed (the un-highlight tool).
 
 import 'package:flutter/foundation.dart'
     show ValueListenable, visibleForTesting;
@@ -30,7 +32,7 @@ import 'package:uuid/uuid.dart';
 import '../../l10n/app_localizations.dart';
 import '../../models/scratch_link.dart';
 import '../../screens/split_view_screen.dart';
-import '../../services/database_service.dart';
+import '../../storage/badnote_sidecar.dart';
 import '../engine/brush.dart';
 import '../engine/shape_geometry.dart';
 import '../engine/stroke_eraser.dart';
@@ -44,8 +46,7 @@ import '../input/pen_input_service.dart';
 import '../input/pressure_curve.dart'
     show PressureCurve, kNaturalPressureFloor;
 import '../pdf/pen_capture_region.dart';
-import '../persistence/editor_repository.dart';
-import '../persistence/save_scheduler.dart';
+import '../persistence/sidecar_repository.dart';
 import '../ui/pen_settings_page.dart';
 import '../ui/thumbnail_grid.dart';
 import 'editor_tool.dart';
@@ -55,23 +56,10 @@ import 'pen_palette_widgets.dart';
 import 'pen_stroke.dart';
 import 'pinch_scale_solver.dart';
 
-/// Stable deterministic document-id for a file path (djb2 hash → hex).
-///
-/// Produces a fixed-length hex string from the path so the id is filesystem-
-/// independent (no slashes, spaces, or non-ASCII characters) and stable across
-/// restarts. Collisions are astronomically unlikely for a single-user app.
 /// On-screen size (px) of a scratch-link anchor marker. Fixed in screen space
 /// (not scaled with zoom) so the tap target stays comfortably tappable.
 const double _kMarkerSize = 36.0;
 
-String _documentIdFromPath(String path) {
-  var hash = 5381;
-  for (final c in path.codeUnits) {
-    hash = ((hash << 5) + hash + c) & 0xFFFFFFFF;
-  }
-  return hash.toRadixString(16).padLeft(8, '0');
-}
-
 class PenEditorScreen extends StatefulWidget {
   const PenEditorScreen({
     super.key,
@@ -109,7 +97,8 @@ class _PenEditorScreenState extends State<PenEditorScreen> {
 
   /// Text highlights per page, keyed by 0-based page index. Each Rect is in
   /// NORMALIZED page coords (left/top/right/bottom in [0,1]) so it stays glued
-  /// under zoom. In-memory only for now — see TODO(persist-highlights).
+  /// under zoom. Persisted to the sidecar (Phase 2 — highlights now survive
+  /// reopen and can be removed via the un-highlight tool).
   final Map<int, List<Rect>> _highlightsByPage = {};
 
   /// Per-page undo/redo history. Snapshot-before-change discipline: the
@@ -125,10 +114,10 @@ class _PenEditorScreenState extends State<PenEditorScreen> {
 
   // ── Persistence ────────────────────────────────────────────────────────────
 
-  /// Stable document-id derived from the PDF file path.
-  late final String _documentId;
-
-  SaveScheduler? _saveScheduler;
+  /// Per-file sidecar persistence. Identity is the source file PATH (the
+  /// sidecar IS the identity — no more djb2 path-hash document id). Null until
+  /// [_initPersistence] resolves.
+  SidecarRepository? _repo;
 
   /// Repaint signal for the page overlays. Bumped on every pen move/commit/erase
   /// and on every viewer transform so the per-page CustomPaint re-projects the
@@ -250,6 +239,11 @@ class _PenEditorScreenState extends State<PenEditorScreen> {
   /// so the tap is handled by the per-page GestureDetector overlay.
   bool _placeLinkMode = false;
 
+  /// When true the "remove highlight" tool is active: a tap on an existing
+  /// highlight rect deletes it (the un-highlight action). Pen capture is
+  /// disabled so the tap is handled by the per-page GestureDetector overlay.
+  bool _removeHighlightMode = false;
+
   /// All scratch-link anchors for this document, loaded on open and updated on
   /// add/delete. Rendered as tappable markers in [pageOverlaysBuilder].
   final List<ScratchLink> _scratchLinks = [];
@@ -279,7 +273,8 @@ class _PenEditorScreenState extends State<PenEditorScreen> {
   /// True when an ink tool (brush/highlighter/eraser/select/shape) is active —
   /// pen capture is on. False in select-text mode (pen reaches pdfrx text
   /// selection) and in place-link mode (a tap drops an anchor via the overlay).
-  bool get _penCaptureEnabled => !_selectTextMode && !_placeLinkMode;
+  bool get _penCaptureEnabled =>
+      !_selectTextMode && !_placeLinkMode && !_removeHighlightMode;
 
   /// True when the eraser tool is active.
   bool get _isEraser => _tool == EditorToolKind.eraser && !_selectTextMode;
@@ -294,7 +289,6 @@ class _PenEditorScreenState extends State<PenEditorScreen> {
   @override
   void initState() {
     super.initState();
-    _documentId = _documentIdFromPath(widget.pdfPath);
     // Begin listening to the native Windows pen plugin (barrel/eraser/tilt).
     // No-op on platforms without the plugin (W3).
     PenInputService.instance.start();
@@ -320,42 +314,25 @@ class _PenEditorScreenState extends State<PenEditorScreen> {
   }
 
   Future<void> _initPersistence() async {
-    final service = await DatabaseService.getInstance();
-    if (!mounted) return;
-    final repo = await EditorRepository.fromService(service);
-    final scheduler = SaveScheduler(repo);
+    final repo = await SidecarRepository.open(widget.pdfPath, docType: 'pdf');
     if (!mounted) {
-      scheduler.dispose();
+      repo.dispose();
       return;
     }
-    _saveScheduler = scheduler;
-    await _loadPersistedStrokes(repo);
-    await _loadScratchLinks(service);
+    _repo = repo;
+    _loadFromSidecar(repo);
   }
 
-  /// Load this document's scratch-link anchors into [_scratchLinks].
-  Future<void> _loadScratchLinks(DatabaseService service) async {
-    final links = await service.loadScratchLinks(_documentId);
-    if (!mounted) return;
-    setState(() {
-      _scratchLinks
-        ..clear()
-        ..addAll(links);
-    });
-  }
-
-  /// Load all persisted strokes for [_documentId] and populate [_strokesByPage].
-  Future<void> _loadPersistedStrokes(EditorRepository repo) async {
-    final hosted = await repo.loadDocument(_documentId);
-    if (!mounted) return;
-    final loaded = <int, List<PenStroke>>{};
-    for (final entry in hosted.entries) {
-      final pageIndex = _pageIndexFromHostId(entry.key);
-      if (pageIndex == null) continue;
-      loaded[pageIndex] = entry.value
+  /// Hydrate the in-memory editor state from the sidecar [repo] loaded on open:
+  /// per-page strokes, per-page highlights, and scratch-link anchors.
+  void _loadFromSidecar(SidecarRepository repo) {
+    final loadedStrokes = <int, List<PenStroke>>{};
+    for (final entry in repo.loadedStrokes.entries) {
+      loadedStrokes[entry.key] = entry.value
           .map((es) => PenStroke(
                 points: es.points
-                    .map((ep) => PenPoint(ep.x, ep.y, ep.pressure, tilt: ep.tilt))
+                    .map((ep) =>
+                        PenPoint(ep.x, ep.y, ep.pressure, tilt: ep.tilt))
                     .toList(),
                 color: es.color,
                 width: es.width,
@@ -372,32 +349,34 @@ class _PenEditorScreenState extends State<PenEditorScreen> {
               ))
           .toList();
     }
-    if (loaded.isNotEmpty) {
-      setState(() {
-        for (final entry in loaded.entries) {
-          _strokesByPage[entry.key] = entry.value;
-        }
-      });
-      _bumpOverlay();
-    }
-  }
 
-  /// Extract the page index from a host_id of the form
-  /// `"doc:<documentId>:page:<pageIndex>"`.
-  int? _pageIndexFromHostId(String hostId) {
-    const marker = ':page:';
-    final idx = hostId.lastIndexOf(marker);
-    if (idx == -1) return null;
-    return int.tryParse(hostId.substring(idx + marker.length));
+    final loadedHighlights = <int, List<Rect>>{};
+    for (final entry in repo.loadedHighlights.entries) {
+      loadedHighlights[entry.key] =
+          entry.value.map((h) => h.toRect()).toList();
+    }
+
+    setState(() {
+      for (final entry in loadedStrokes.entries) {
+        _strokesByPage[entry.key] = entry.value;
+      }
+      for (final entry in loadedHighlights.entries) {
+        _highlightsByPage[entry.key] = entry.value;
+      }
+      _scratchLinks
+        ..clear()
+        ..addAll(repo.loadedScratchLinks.map((s) => s.link));
+    });
+    _bumpOverlay();
   }
 
   @override
   void dispose() {
-    // Flush any pending scheduled saves before tearing down.
-    final scheduler = _saveScheduler;
-    if (scheduler != null) {
-      scheduler.flush(); // fire-and-forget; DB write continues in isolate
-      scheduler.dispose();
+    // Flush any pending sidecar write before tearing down.
+    final repo = _repo;
+    if (repo != null) {
+      repo.flush(); // fire-and-forget; atomic write completes off the UI tree
+      repo.dispose();
     }
     _overlayRepaint.dispose();
     _liveStrokeVN.dispose();
@@ -446,18 +425,14 @@ class _PenEditorScreenState extends State<PenEditorScreen> {
     _bumpOverlay();
   }
 
-  /// Convert [strokes] to [EditorStroke]s and hand them to the save scheduler.
+  /// Convert [strokes] to [EditorStroke]s and hand them to the sidecar repo.
   void _schedulePageSave(int pageIndex, List<PenStroke> strokes) {
-    final scheduler = _saveScheduler;
-    if (scheduler == null) return;
+    final repo = _repo;
+    if (repo == null) return;
     final editorStrokes = strokes
         .map((s) => simplifyStroke(EditorStroke.fromPenStroke(s)))
         .toList();
-    scheduler.schedule(
-      'page',
-      EditorRepository.pageHostId(_documentId, pageIndex),
-      editorStrokes,
-    );
+    repo.scheduleStrokeSave(pageIndex, editorStrokes);
   }
 
   void _performUndo() {
@@ -917,12 +892,52 @@ class _PenEditorScreenState extends State<PenEditorScreen> {
       }
       _hasSelection = false;
     });
-    // TODO(persist-highlights): highlights are in-memory only; wire them into
-    // EditorRepository (a new host_kind) for cross-session persistence.
+    // Persist each touched page's highlights to the sidecar (Phase 2 — closes
+    // the old in-memory-only limitation; highlights now survive reopen).
+    for (final pageIndex in added.keys) {
+      _scheduleHighlightSave(pageIndex);
+    }
     await delegate.clearTextSelection();
     _bumpOverlay();
   }
 
+  /// Serialize the current highlights for [pageIndex] to the sidecar.
+  void _scheduleHighlightSave(int pageIndex) {
+    final repo = _repo;
+    if (repo == null) return;
+    final rects = _highlightsByPage[pageIndex] ?? const <Rect>[];
+    repo.scheduleHighlightSave(
+      pageIndex,
+      rects.map((r) => SidecarHighlight.fromRect(r)).toList(),
+    );
+  }
+
+  /// Remove the highlight rect on [pageIndex] under the normalized point
+  /// [normalized] (topmost hit), persisting the change. Returns true if one was
+  /// removed. This is the "un-highlight" action (a stored highlight could not be
+  /// removed before): in SELECT-TEXT mode a tap on an existing highlight erases
+  /// it.
+  bool _removeHighlightAt(int pageIndex, Offset normalized) {
+    final rects = _highlightsByPage[pageIndex];
+    if (rects == null || rects.isEmpty) return false;
+    for (var i = rects.length - 1; i >= 0; i--) {
+      if (rects[i].contains(normalized)) {
+        setState(() {
+          final next = List<Rect>.of(rects)..removeAt(i);
+          if (next.isEmpty) {
+            _highlightsByPage.remove(pageIndex);
+          } else {
+            _highlightsByPage[pageIndex] = next;
+          }
+        });
+        _scheduleHighlightSave(pageIndex);
+        _bumpOverlay();
+        return true;
+      }
+    }
+    return false;
+  }
+
   // ── Navigation / tools ─────────────────────────────────────────────────────
 
   void _goToPage(int index) {
@@ -936,6 +951,7 @@ class _PenEditorScreenState extends State<PenEditorScreen> {
       _tool = tool;
       _selectTextMode = false;
       _placeLinkMode = false;
+      _removeHighlightMode = false;
       if (tool != EditorToolKind.select) _selected = null;
     });
   }
@@ -944,6 +960,7 @@ class _PenEditorScreenState extends State<PenEditorScreen> {
     setState(() {
       _selectTextMode = true;
       _placeLinkMode = false;
+      _removeHighlightMode = false;
       _selected = null;
     });
   }
@@ -953,7 +970,23 @@ class _PenEditorScreenState extends State<PenEditorScreen> {
   void _togglePlaceLinkMode() {
     setState(() {
       _placeLinkMode = !_placeLinkMode;
-      if (_placeLinkMode) _selectTextMode = false;
+      if (_placeLinkMode) {
+        _selectTextMode = false;
+        _removeHighlightMode = false;
+      }
+    });
+  }
+
+  /// Toggle "remove highlight" mode (the un-highlight action). While active, a
+  /// tap on an existing highlight deletes it (persisted to the sidecar).
+  void _toggleRemoveHighlightMode() {
+    setState(() {
+      _removeHighlightMode = !_removeHighlightMode;
+      if (_removeHighlightMode) {
+        _selectTextMode = false;
+        _placeLinkMode = false;
+        _selected = null;
+      }
     });
   }
 
@@ -964,30 +997,48 @@ class _PenEditorScreenState extends State<PenEditorScreen> {
   Future<void> _placeScratchLink(int pageIndex, Offset normalized) async {
     final link = ScratchLink(
       id: _uuid.v4(),
-      documentId: _documentId,
+      // The source file path is the identity now (the sidecar IS the identity);
+      // documentId is retained on the model only so the split view can address
+      // the source PDF. Use the file path so it's stable across reopen.
+      documentId: widget.pdfPath,
       pageIndex: pageIndex,
       nx: normalized.dx.clamp(0.0, 1.0),
       ny: normalized.dy.clamp(0.0, 1.0),
     );
-    final service = await DatabaseService.getInstance();
-    await service.saveScratchLink(link);
+    _repo?.scheduleScratchLinkUpsert(link);
     if (!mounted) return;
     setState(() => _scratchLinks.add(link));
   }
 
   /// Open the anchor's split view (left = this PDF at the anchor page, right =
-  /// the anchor's private infinite scratchpad).
-  void _openScratchLink(ScratchLink link) {
-    Navigator.of(context).push(
+  /// the anchor's private infinite scratchpad, stored in the sidecar).
+  ///
+  /// Flushes any pending sidecar write FIRST so the split view (which opens its
+  /// own [SidecarRepository] on the same file) sees this anchor on disk before
+  /// it writes the scratchpad back. On return, reload so any scratchpad change
+  /// made there is reflected in this editor's in-memory sidecar repo.
+  Future<void> _openScratchLink(ScratchLink link) async {
+    await _repo?.flush();
+    if (!mounted) return;
+    await Navigator.of(context).push(
       MaterialPageRoute(
         builder: (_) => SplitViewScreen(
           filePath: widget.pdfPath,
-          documentId: _documentId,
           scratchLinkId: link.id,
           initialPage: link.pageIndex,
         ),
       ),
     );
+    if (!mounted) return;
+    // The split view wrote the scratchpad into the on-disk sidecar via its own
+    // repo; re-open ours so subsequent saves here don't clobber that scratchpad.
+    final repo = await SidecarRepository.open(widget.pdfPath, docType: 'pdf');
+    if (!mounted) {
+      repo.dispose();
+      return;
+    }
+    _repo?.dispose();
+    _repo = repo;
   }
 
   /// Confirm + delete an anchor (and its private scratchpad).
@@ -1011,8 +1062,7 @@ class _PenEditorScreenState extends State<PenEditorScreen> {
       ),
     );
     if (confirmed != true) return;
-    final service = await DatabaseService.getInstance();
-    await service.deleteScratchLink(link.id);
+    _repo?.scheduleScratchLinkDelete(link.id);
     if (!mounted) return;
     setState(() => _scratchLinks.removeWhere((s) => s.id == link.id));
   }
@@ -1168,6 +1218,22 @@ class _PenEditorScreenState extends State<PenEditorScreen> {
                   },
                 ),
               ),
+            // Tap-to-remove-highlight layer (the un-highlight action): only
+            // swallows taps while remove-highlight mode is on; a tap on an
+            // existing highlight deletes it (persisted to the sidecar).
+            if (_removeHighlightMode)
+              Positioned.fill(
+                child: GestureDetector(
+                  behavior: HitTestBehavior.opaque,
+                  onTapUp: (details) {
+                    final local = details.localPosition;
+                    if (pageW <= 0 || pageH <= 0) return;
+                    final nx = (local.dx / pageW).clamp(0.0, 1.0);
+                    final ny = (local.dy / pageH).clamp(0.0, 1.0);
+                    _removeHighlightAt(pageIndex, Offset(nx, ny));
+                  },
+                ),
+              ),
             // Anchor markers (sticky-note tabs): tap → split view, long-press →
             // delete. Sized in screen px so the tap target stays usable at any
             // zoom; positioned at (nx*pageW, ny*pageH).
@@ -1297,6 +1363,14 @@ class _PenEditorScreenState extends State<PenEditorScreen> {
               tooltip: l.actionHighlightSelection,
               onPressed: _hasSelection ? _highlightSelection : null,
             ),
+            // Un-highlight: toggle a mode where tapping an existing highlight
+            // removes it (the user couldn't remove highlights before).
+            ToolButton(
+              icon: Icons.highlight_off,
+              selected: _removeHighlightMode,
+              tooltip: l.toolRemoveHighlight,
+              onPressed: _toggleRemoveHighlightMode,
+            ),
             PaletteDivider(cs: cs),
             // Place scratch link (sticky-note tab). Tap a page to drop an anchor.
             ToolButton(

lib/editor/persistence/sidecar_repository.dart

@@ -0,0 +1,216 @@
+// lib/editor/persistence/sidecar_repository.dart
+//
+// Phase 2 of the file-based storage plan (docs/plans/2026-06-24-file-based-
+// storage.md §F): the PDF editor's persistence sink. Replaces the SQLite-backed
+// EditorRepository/SaveScheduler/DatabaseService trio for the pen editor with a
+// single per-file SIDECAR (`<sourceFile>.badnote.json`) living ALONGSIDE the
+// source file, so annotations travel with the file ("跟着文件走").
+//
+// Design:
+//   * The repository owns the canonical in-memory [BadnoteSidecar]. Callers
+//     mutate it through the schedule* methods, which (1) update the in-memory
+//     model SYNCHRONOUSLY (so the snapshot can't be corrupted by a later edit
+//     mid-write — the SaveScheduler discipline, §F.2) and (2) arm a single
+//     debounce timer that writes the WHOLE sidecar atomically (§F.1, via
+//     SidecarStore.writeAtomic — temp + rename + .bak).
+//   * The unit of debounce is the whole document sidecar (sidecars are small —
+//     sparse normalized strokes), one atomic write per debounce window.
+//   * Identity is the SOURCE FILE PATH, not the old djb2 path-hash document id.
+//     The sidecar IS the identity.
+
+import 'dart:async';
+import 'dart:io';
+
+import '../../models/scratch_link.dart';
+import '../../storage/badnote_sidecar.dart';
+import '../../storage/sidecar_store.dart';
+import '../engine/stroke_model.dart';
+
+/// Suffix appended to a source-file path to form its sidecar path.
+const String kSidecarSuffix = '.badnote.json';
+
+/// Per-file persistence for the pen editor. Loads the sidecar for a source file
+/// path, holds it in memory, and debounces atomic writes back to disk.
+class SidecarRepository {
+  SidecarRepository._({
+    required this.sourceFilePath,
+    required BadnoteSidecar sidecar,
+    Duration debounce = const Duration(milliseconds: 800),
+  })  : _sidecar = sidecar,
+        _debounce = debounce;
+
+  /// Absolute path to the annotated source file (e.g. the vault PDF copy).
+  final String sourceFilePath;
+
+  /// The sidecar file: `<sourceFilePath>.badnote.json`.
+  File get sidecarFile => File('$sourceFilePath$kSidecarSuffix');
+
+  final Duration _debounce;
+
+  BadnoteSidecar _sidecar;
+  Timer? _timer;
+  bool _disposed = false;
+
+  /// Open (or create) the repository for [sourceFilePath]. Reads the existing
+  /// sidecar if present (falling back to its `.bak`), else starts empty.
+  static Future<SidecarRepository> open(
+    String sourceFilePath, {
+    String? docType,
+    Duration debounce = const Duration(milliseconds: 800),
+  }) async {
+    final file = File('$sourceFilePath$kSidecarSuffix');
+    final existing = await SidecarStore.read(file);
+    final sidecar = existing ??
+        BadnoteSidecar(
+          sourceFile: _basename(sourceFilePath),
+          docType: docType,
+          createdAt: DateTime.now().toUtc(),
+        );
+    return SidecarRepository._(
+      sourceFilePath: sourceFilePath,
+      sidecar: sidecar,
+      debounce: debounce,
+    );
+  }
+
+  // ── Loaded snapshot accessors (read at open) ───────────────────────────────
+
+  /// Page index → committed strokes loaded from the sidecar.
+  Map<int, List<EditorStroke>> get loadedStrokes => _sidecar.strokes;
+
+  /// Page index → highlight rects loaded from the sidecar.
+  Map<int, List<SidecarHighlight>> get loadedHighlights => _sidecar.highlights;
+
+  /// Scratch-link anchors loaded from the sidecar.
+  List<SidecarScratchLink> get loadedScratchLinks => _sidecar.scratchLinks;
+
+  /// The current in-memory sidecar (for tests / inspection).
+  BadnoteSidecar get sidecar => _sidecar;
+
+  // ── Mutations (synchronous in-memory update + debounced atomic write) ──────
+
+  /// Replace the committed strokes for [pageIndex] and schedule a save.
+  void scheduleStrokeSave(int pageIndex, List<EditorStroke> strokes) {
+    final next = Map<int, List<EditorStroke>>.from(_sidecar.strokes);
+    if (strokes.isEmpty) {
+      next.remove(pageIndex);
+    } else {
+      next[pageIndex] = List<EditorStroke>.of(strokes);
+    }
+    _replace(strokes: next);
+  }
+
+  /// Replace the highlight rects for [pageIndex] and schedule a save.
+  void scheduleHighlightSave(int pageIndex, List<SidecarHighlight> highlights) {
+    final next = Map<int, List<SidecarHighlight>>.from(_sidecar.highlights);
+    if (highlights.isEmpty) {
+      next.remove(pageIndex);
+    } else {
+      next[pageIndex] = List<SidecarHighlight>.of(highlights);
+    }
+    _replace(highlights: next);
+  }
+
+  /// Add (or update) a scratch-link anchor, preserving any existing scratchpad,
+  /// and schedule a save.
+  void scheduleScratchLinkUpsert(ScratchLink link) {
+    final next = List<SidecarScratchLink>.of(_sidecar.scratchLinks);
+    final idx = next.indexWhere((s) => s.link.id == link.id);
+    if (idx == -1) {
+      next.add(SidecarScratchLink(link: link));
+    } else {
+      next[idx] = SidecarScratchLink(
+        link: link,
+        scratchpad: next[idx].scratchpad,
+      );
+    }
+    _replace(scratchLinks: next);
+  }
+
+  /// Remove the scratch-link anchor (and its embedded scratchpad) by [linkId].
+  void scheduleScratchLinkDelete(String linkId) {
+    final next = _sidecar.scratchLinks
+        .where((s) => s.link.id != linkId)
+        .toList(growable: false);
+    _replace(scratchLinks: List<SidecarScratchLink>.of(next));
+  }
+
+  /// Replace the embedded scratchpad of the anchor [linkId] and schedule a save.
+  /// No-op if the anchor isn't present.
+  void scheduleScratchpadSave(String linkId, SidecarScratchpad scratchpad) {
+    final next = List<SidecarScratchLink>.of(_sidecar.scratchLinks);
+    final idx = next.indexWhere((s) => s.link.id == linkId);
+    if (idx == -1) return;
+    next[idx] = SidecarScratchLink(link: next[idx].link, scratchpad: scratchpad);
+    _replace(scratchLinks: next);
+  }
+
+  /// The embedded scratchpad for [linkId], or null if the anchor is unknown.
+  SidecarScratchpad? scratchpadFor(String linkId) {
+    for (final s in _sidecar.scratchLinks) {
+      if (s.link.id == linkId) return s.scratchpad;
+    }
+    return null;
+  }
+
+  // ── Flush / dispose ────────────────────────────────────────────────────────
+
+  /// Write any pending change immediately and wait for it to land.
+  Future<void> flush() async {
+    if (_timer == null) return;
+    _timer!.cancel();
+    _timer = null;
+    await _write();
+  }
+
+  /// Cancel pending timers. Call [flush] first to persist pending writes.
+  void dispose() {
+    _disposed = true;
+    _timer?.cancel();
+    _timer = null;
+  }
+
+  // ── Internal ───────────────────────────────────────────────────────────────
+
+  /// Build a new sidecar (touching `updatedAt`) from the current one with the
+  /// given fields replaced, then arm the debounce timer. Snapshot is captured
+  /// synchronously here so a later edit can't corrupt an in-flight write.
+  void _replace({
+    Map<int, List<EditorStroke>>? strokes,
+    Map<int, List<SidecarHighlight>>? highlights,
+    List<SidecarScratchLink>? scratchLinks,
+  }) {
+    if (_disposed) return;
+    _sidecar = BadnoteSidecar(
+      version: _sidecar.version,
+      sourceFile: _sidecar.sourceFile,
+      docType: _sidecar.docType,
+      pageCount: _sidecar.pageCount,
+      rotation: _sidecar.rotation,
+      createdAt: _sidecar.createdAt,
+      updatedAt: DateTime.now().toUtc(),
+      strokes: strokes ?? _sidecar.strokes,
+      highlights: highlights ?? _sidecar.highlights,
+      bookmarks: _sidecar.bookmarks,
+      scratchLinks: scratchLinks ?? _sidecar.scratchLinks,
+    );
+    _timer?.cancel();
+    _timer = Timer(_debounce, () {
+      _timer = null;
+      // Fire-and-forget; the next schedule simply re-arms the timer and the
+      // atomic write guarantees no torn file.
+      _write();
+    });
+  }
+
+  Future<void> _write() async {
+    final snapshot = _sidecar;
+    await SidecarStore.writeAtomic(sidecarFile, snapshot);
+  }
+
+  static String _basename(String path) {
+    final norm = path.replaceAll('\\', '/');
+    final i = norm.lastIndexOf('/');
+    return i == -1 ? norm : norm.substring(i + 1);
+  }
+}

lib/l10n/app_en.arb

@@ -71,6 +71,7 @@
   "nextPage": "Next page",
   "toolSelectText": "Select text",
   "actionHighlightSelection": "Highlight selection",
+  "toolRemoveHighlight": "Remove highlight (tap a highlight)",
   "toolPlaceScratchLink": "Place scratch link",
   "scratchLinkDeleteTitle": "Delete scratch link?",
   "scratchLinkDeleteBody": "This removes the anchor and its private scratchpad.",

lib/l10n/app_localizations.dart

@@ -470,6 +470,12 @@ abstract class AppLocalizations {
   /// **'Highlight selection'**
   String get actionHighlightSelection;
 
+  /// No description provided for @toolRemoveHighlight.
+  ///
+  /// In en, this message translates to:
+  /// **'Remove highlight (tap a highlight)'**
+  String get toolRemoveHighlight;
+
   /// No description provided for @toolPlaceScratchLink.
   ///
   /// In en, this message translates to:

lib/l10n/app_localizations_en.dart

@@ -200,6 +200,9 @@ class AppLocalizationsEn extends AppLocalizations {
   @override
   String get actionHighlightSelection => 'Highlight selection';
 
+  @override
+  String get toolRemoveHighlight => 'Remove highlight (tap a highlight)';
+
   @override
   String get toolPlaceScratchLink => 'Place scratch link';
 

lib/l10n/app_localizations_zh.dart

@@ -200,6 +200,9 @@ class AppLocalizationsZh extends AppLocalizations {
   @override
   String get actionHighlightSelection => '高亮所选';
 
+  @override
+  String get toolRemoveHighlight => '移除高亮（点按高亮处）';
+
   @override
   String get toolPlaceScratchLink => '放置便签链接';
 

lib/l10n/app_zh.arb

@@ -62,6 +62,7 @@
   "nextPage": "下一页",
   "toolSelectText": "选择文字",
   "actionHighlightSelection": "高亮所选",
+  "toolRemoveHighlight": "移除高亮（点按高亮处）",
   "toolPlaceScratchLink": "放置便签链接",
   "scratchLinkDeleteTitle": "删除便签链接？",
   "scratchLinkDeleteBody": "这会移除锚点及其专属草稿纸。",

lib/screens/split_view_screen.dart

@@ -13,7 +13,6 @@
 // ToolButton / color dots), replacing the old AnnotationToolbar.
 
 import 'dart:async';
-import 'dart:convert';
 
 import 'package:flutter/material.dart';
 import 'package:pdfrx/pdfrx.dart';
@@ -25,21 +24,22 @@ import '../editor/canvas/pen_stroke.dart';
 import '../editor/engine/brush.dart';
 import '../editor/input/pen_config.dart' show kDefaultEraserRadius;
 import '../editor/notebook/ink_stroke_adapter.dart';
+import '../editor/persistence/sidecar_repository.dart';
 import '../models/ink_stroke.dart';
-import '../services/database_service.dart';
 import '../services/undo_manager.dart';
+import '../storage/badnote_sidecar.dart';
 
 /// Split-view derivation surface for a single scratch-link anchor: left pane =
 /// the reference PDF (at [initialPage]), right pane = the anchor's private
-/// infinite scratchpad. Scratchpad strokes persist per ANCHOR via
-/// [DatabaseService.saveScratchpad] / [DatabaseService.loadScratchpad], keyed by
-/// [scratchLinkId].
+/// infinite scratchpad. Scratchpad strokes persist inside the source file's
+/// SIDECAR (`<filePath>.badnote.json`), embedded in the anchor's
+/// `scratchLinks[id].scratchpad` (keyed by [scratchLinkId]). Strokes keep the
+/// absolute world-pixel [InkStroke] format unchanged.
 class SplitViewScreen extends StatefulWidget {
   final String filePath;
-  final String documentId;
 
-  /// The owning anchor id. Doubles as the scratchpad storage key so this is the
-  /// anchor's private scratch space.
+  /// The owning anchor id. Selects which `scratchLinks[].scratchpad` in the
+  /// sidecar this is the private scratch space for.
   final String scratchLinkId;
 
   /// 0-based page the anchor sits on; the left PDF opens here.
@@ -48,7 +48,6 @@ class SplitViewScreen extends StatefulWidget {
   const SplitViewScreen({
     super.key,
     required this.filePath,
-    required this.documentId,
     required this.scratchLinkId,
     this.initialPage = 0,
   });
@@ -102,6 +101,11 @@ class _SplitViewState extends State<SplitViewScreen> {
   Timer? _saveTimer;
   bool _dirty = false;
 
+  /// Sidecar persistence for the source file (the scratchpad is embedded in the
+  /// anchor's `scratchLinks[id].scratchpad`). Null until [_loadScratchpad]
+  /// resolves.
+  SidecarRepository? _repo;
+
   static const double _edgeThreshold = 200.0;
   static const double _expandAmount = 1000.0;
 
@@ -116,18 +120,34 @@ class _SplitViewState extends State<SplitViewScreen> {
   void dispose() {
     _saveTimer?.cancel();
     _saveImmediate();
+    final repo = _repo;
+    if (repo != null) {
+      repo.flush(); // fire-and-forget; atomic write finishes off the tree
+      repo.dispose();
+    }
     // PdfViewerController (pdfrx) has no dispose(); it detaches with the viewer.
     _scratchTransform.dispose();
     super.dispose();
   }
 
-  // -- Persistence (keyed by the ANCHOR id, not the documentId) --
+  // -- Persistence (sidecar's scratchLinks[id].scratchpad, keyed by anchor id) --
 
   Future<void> _loadScratchpad() async {
-    final db = await DatabaseService.getInstance();
-    final strokes = await db.loadScratchpad(widget.scratchLinkId);
-    if (!mounted) return;
+    final repo = await SidecarRepository.open(widget.filePath, docType: 'pdf');
+    if (!mounted) {
+      repo.dispose();
+      return;
+    }
+    _repo = repo;
+    final pad = repo.scratchpadFor(widget.scratchLinkId);
     setState(() {
+      if (pad != null) {
+        // Restore the world size so the infinite canvas reopens at its grown
+        // extent (previously always reset to 4000×4000).
+        _canvasWidth = pad.canvasWidth;
+        _canvasHeight = pad.canvasHeight;
+      }
+      final strokes = pad?.strokes ?? const <InkStroke>[];
       // Keep only freehand strokes so the canvas list stays 1:1 with the undo
       // manager (shapes/text have no pen-canvas representation).
       final freehand = strokes.where((s) => isFreehandTool(s.tool)).toList();
@@ -147,9 +167,17 @@ class _SplitViewState extends State<SplitViewScreen> {
   Future<void> _saveImmediate() async {
     if (!_dirty) return;
     _dirty = false;
-    final db = await DatabaseService.getInstance();
-    final json = jsonEncode(_strokes.map((s) => s.toJson()).toList());
-    await db.saveScratchpad(widget.scratchLinkId, json);
+    final repo = _repo;
+    if (repo == null) return;
+    repo.scheduleScratchpadSave(
+      widget.scratchLinkId,
+      SidecarScratchpad(
+        canvasWidth: _canvasWidth,
+        canvasHeight: _canvasHeight,
+        strokes: List<InkStroke>.of(_strokes),
+      ),
+    );
+    await repo.flush();
   }
 
   // -- Scratchpad stroke callbacks --

test/sidecar_repository_test.dart

@@ -0,0 +1,203 @@
+// test/sidecar_repository_test.dart
+//
+// Phase 2: SidecarRepository is the pen editor's persistence sink (replacing the
+// SQLite EditorRepository / DatabaseService scratch storage). These tests drive
+// the repository directly with a tiny debounce + flush() so writes are
+// deterministic, then RE-OPEN the same file and assert everything restored:
+//   * per-page strokes
+//   * per-page highlights (the previously in-memory-only data)
+//   * scratch-link anchors + their embedded scratchpad ink (absolute world px)
+//   * removing a highlight persists (the "un-highlight" action)
+
+import 'dart:io';
+
+import 'package:flutter_test/flutter_test.dart';
+
+import 'package:badnote/editor/engine/stroke_model.dart';
+import 'package:badnote/editor/persistence/sidecar_repository.dart';
+import 'package:badnote/models/ink_point.dart';
+import 'package:badnote/models/ink_stroke.dart';
+import 'package:badnote/models/pen_tool.dart';
+import 'package:badnote/models/scratch_link.dart';
+import 'package:badnote/storage/badnote_sidecar.dart';
+
+const _fast = Duration(milliseconds: 1);
+
+EditorStroke _stroke(String id, {EditorTool tool = EditorTool.pen}) =>
+    EditorStroke(
+      id: id,
+      points: const [
+        EditorPoint(x: 0.1, y: 0.2, pressure: 0.5),
+        EditorPoint(x: 0.3, y: 0.4, pressure: 0.7),
+      ],
+      tool: tool,
+      color: 0xFF112233,
+      width: 0.005,
+    );
+
+InkStroke _ink(String id, double x) => InkStroke(
+      id: id,
+      points: [InkPoint(x: x, y: x + 1, timestamp: 0)],
+      tool: PenTool.pen,
+      createdAt: DateTime.utc(2026, 1, 1),
+    );
+
+void main() {
+  late Directory tmpDir;
+  late String src;
+
+  setUp(() async {
+    tmpDir = await Directory.systemTemp.createTemp('sidecar_repo_test');
+    src = '${tmpDir.path}/Lecture.pdf';
+    // The source file doesn't have to exist for the sidecar to work, but create
+    // it so the layout matches reality (sidecar lives alongside the file).
+    await File(src).writeAsString('%PDF-1.7 fake');
+  });
+
+  tearDown(() async {
+    if (await tmpDir.exists()) await tmpDir.delete(recursive: true);
+  });
+
+  test('sidecar path is <sourceFile>.badnote.json alongside the file', () async {
+    final repo = await SidecarRepository.open(src, debounce: _fast);
+    expect(repo.sidecarFile.path, '$src.badnote.json');
+    repo.dispose();
+  });
+
+  test('strokes + highlight + scratch-link + scratchpad restore on reopen',
+      () async {
+    final repo = await SidecarRepository.open(src, debounce: _fast);
+
+    // Page 0 strokes.
+    repo.scheduleStrokeSave(0, [_stroke('a'), _stroke('b')]);
+    // Page 0 highlight (normalized rect).
+    repo.scheduleHighlightSave(
+      0,
+      const [SidecarHighlight(l: 0.1, t: 0.15, r: 0.8, b: 0.2, color: 0xFFFFFF00)],
+    );
+    // A scratch-link anchor on page 3, then its private scratchpad ink.
+    const link = ScratchLink(
+      id: 'anchor-1',
+      documentId: 'ignored-uses-path',
+      pageIndex: 3,
+      nx: 0.5,
+      ny: 0.5,
+    );
+    repo.scheduleScratchLinkUpsert(link);
+    repo.scheduleScratchpadSave(
+      'anchor-1',
+      SidecarScratchpad(
+        canvasWidth: 5000,
+        canvasHeight: 6000,
+        strokes: [_ink('w0', 100), _ink('w1', 200)],
+      ),
+    );
+    await repo.flush();
+    repo.dispose();
+
+    // Re-open the SAME file: everything must come back.
+    final reopened = await SidecarRepository.open(src, debounce: _fast);
+
+    expect(reopened.loadedStrokes[0]?.map((s) => s.id), ['a', 'b']);
+    expect(reopened.loadedStrokes[0]!.first.color, 0xFF112233);
+
+    final hl = reopened.loadedHighlights[0]!.single;
+    expect(hl.l, 0.1);
+    expect(hl.r, 0.8);
+    expect(hl.color, 0xFFFFFF00);
+
+    final sl = reopened.loadedScratchLinks.single;
+    expect(sl.link.id, 'anchor-1');
+    expect(sl.link.pageIndex, 3);
+    expect(sl.scratchpad.canvasWidth, 5000);
+    expect(sl.scratchpad.canvasHeight, 6000);
+    expect(sl.scratchpad.strokes.map((s) => s.id), ['w0', 'w1']);
+    expect(sl.scratchpad.strokes.first.points.single.x, 100);
+
+    // The scratchpad is addressable by anchor id.
+    expect(reopened.scratchpadFor('anchor-1')!.strokes.length, 2);
+    expect(reopened.scratchpadFor('missing'), isNull);
+
+    reopened.dispose();
+  });
+
+  test('removing a highlight persists (un-highlight)', () async {
+    final repo = await SidecarRepository.open(src, debounce: _fast);
+    repo.scheduleHighlightSave(0, const [
+      SidecarHighlight(l: 0.1, t: 0.1, r: 0.4, b: 0.2),
+      SidecarHighlight(l: 0.5, t: 0.5, r: 0.9, b: 0.6),
+    ]);
+    await repo.flush();
+    repo.dispose();
+
+    // Re-open, drop one highlight (mirrors _removeHighlightAt → save), reopen.
+    final mid = await SidecarRepository.open(src, debounce: _fast);
+    expect(mid.loadedHighlights[0]!.length, 2);
+    final remaining = mid.loadedHighlights[0]!
+        .where((h) => h.l != 0.1) // remove the first
+        .toList();
+    mid.scheduleHighlightSave(0, remaining);
+    await mid.flush();
+    mid.dispose();
+
+    final after = await SidecarRepository.open(src, debounce: _fast);
+    expect(after.loadedHighlights[0]!.length, 1);
+    expect(after.loadedHighlights[0]!.single.l, 0.5);
+    after.dispose();
+  });
+
+  test('removing the last highlight on a page clears the page entry', () async {
+    final repo = await SidecarRepository.open(src, debounce: _fast);
+    repo.scheduleHighlightSave(
+        0, const [SidecarHighlight(l: 0.1, t: 0.1, r: 0.4, b: 0.2)]);
+    await repo.flush();
+    repo.scheduleHighlightSave(0, const []);
+    await repo.flush();
+    repo.dispose();
+
+    final after = await SidecarRepository.open(src, debounce: _fast);
+    expect(after.loadedHighlights.containsKey(0), isFalse);
+    after.dispose();
+  });
+
+  test('deleting a scratch link removes it and its scratchpad', () async {
+    final repo = await SidecarRepository.open(src, debounce: _fast);
+    repo.scheduleScratchLinkUpsert(const ScratchLink(
+      id: 'x',
+      documentId: 'd',
+      pageIndex: 0,
+      nx: 0.2,
+      ny: 0.2,
+    ));
+    repo.scheduleScratchpadSave(
+      'x',
+      SidecarScratchpad(strokes: [_ink('s', 1)]),
+    );
+    await repo.flush();
+    repo.scheduleScratchLinkDelete('x');
+    await repo.flush();
+    repo.dispose();
+
+    final after = await SidecarRepository.open(src, debounce: _fast);
+    expect(after.loadedScratchLinks, isEmpty);
+    after.dispose();
+  });
+
+  test('upserting a scratch link preserves its existing scratchpad', () async {
+    final repo = await SidecarRepository.open(src, debounce: _fast);
+    const link =
+        ScratchLink(id: 'k', documentId: 'd', pageIndex: 1, nx: 0.1, ny: 0.1);
+    repo.scheduleScratchLinkUpsert(link);
+    repo.scheduleScratchpadSave('k', SidecarScratchpad(strokes: [_ink('s', 7)]));
+    // Re-upsert the same anchor (e.g. moved) — scratchpad must survive.
+    repo.scheduleScratchLinkUpsert(link.copyWith(nx: 0.9));
+    await repo.flush();
+    repo.dispose();
+
+    final after = await SidecarRepository.open(src, debounce: _fast);
+    final sl = after.loadedScratchLinks.single;
+    expect(sl.link.nx, 0.9);
+    expect(sl.scratchpad.strokes.single.id, 's');
+    after.dispose();
+  });
+}