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.

tests/extraction.test.ts

@@ -66,6 +66,7 @@ function memoryLedgers() {
 	const checkpoints: SessionCheckpoint[] = [];
 	const sources = new Map<string, NotesSource>();
 	const clusterLabels: ClusterLabeling[] = [];
+	const positions = new Map<string, { x: number; y: number }>();
 	return {
 		appendNode: (n: GraphNode) => void nodes.push(n),
 		readNodes: () => nodes.map((n) => ({ ...n })),
@@ -95,6 +96,12 @@ function memoryLedgers() {
 			if (!clusterLabels.some((x) => x.id === l.id)) clusterLabels.push(l);
 		},
 		readClusterLabels: () => clusterLabels.map((l) => ({ ...l, core: [...l.core] })),
+		// The layout ledger — settleGraphLayout writes it after each merge.
+		readPositions: () => Object.fromEntries([...positions].map(([id, p]) => [id, { ...p }])),
+		writePositions: (next) => {
+			positions.clear();
+			for (const [id, p] of Object.entries(next)) positions.set(id, { x: p.x, y: p.y });
+		},
 	} satisfies GraphStore;
 }