Option A: incremental anchored force layout, persisted server-side

The layout now EVOLVES instead of reshuffling on every extraction. A pure
core module (src/core/layout.ts) warm-starts forceAtlas2 from the positions
ledger (data/graph/positions.json, read-modify-write like sources.json,
updatedAt stamp for future live-physics conflict handling), re-blends every
previously-positioned node toward its anchor each iteration (retention 0.85
- old placements stay recognizable, strong forces still win), seeds new
nodes near their positioned neighbors, and seeds orphans on the rim outside
the core so they read as unconnected knowledge.

- Port/store: GraphStore.readPositions/writePositions; snapshot carries
  positions when the ledger exists (optional - fresh graphs unchanged).
- Extraction pipeline settles synchronously after every merge (chat and
  notes paths), before usage persist - the next /api/graph fetch already
  reflects new nodes.
- View: the ledger IS the layout; the local one-shot FA2 pass survives
  only as a fallback when no ledger exists.
- scripts/replay-layout.ts: simulates organic growth by replaying the
  current 338-node graph one imported file at a time (real import order,
  edges activate when both endpoints exist). Real run: 338 positions in
  0.3s, 90-degree-0 orphans collecting at mean r=338 vs connected r=194.
- Also restores the cluster region fills (hull background colors) that
  6692b19 had removed on a misreading of "no glow".

Live-verified: fit zoom derives from the ledger bbox, pickAt aligns with
ledger positions at every probe, hover/click/detail-card work, 408/408
tests, typecheck/lint/build green.

Future live physics stays cheap by design: the same pure function is the
merge-time settler and the future client simulator; a pinned node is just
an anchor with full retention.

src/core/contracts/graph.ts

@@ -321,6 +321,16 @@ export interface GraphSnapshot {
 	 * joined with persisted LLM labelings. Purely structural — never
 	 * depends on layout. */
 	clusters: Cluster[];
+	/** Resting layout positions per node id, when a positions ledger
+	 *  exists (core/layout.ts settle writes it). Absent on a fresh graph —
+	 *  the view then falls back to its own one-shot forceAtlas2 pass. */
+	positions?: Record<string, Position>;
+}
+
+/** A node's resting position in layout space (the positions ledger). */
+export interface Position {
+	x: number;
+	y: number;
 }
 
 /** Derive a short chat title from the learner's first message (pure).