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/ports.ts

@@ -22,6 +22,7 @@ import type {
 	ExtractionRunUsage,
 	NodeMapping,
 	PlanTree,
+	Position,
 	SessionCheckpoint,
 	TurnUsage,
 	NotesSource,
@@ -96,6 +97,13 @@ export interface GraphStore {
 	/** Append one run's usage to a source record — idempotent per
 	 *  startedAt, mirroring ChatRecord.extractions. */
 	appendSourceUsage(id: string, entry: ExtractionRunUsage): void;
+
+	/** The layout ledger (config.POSITIONS_FILE): nodeId → resting {x,y}.
+	 *  WRITTEN ONLY by the incremental settle after a merge (core/layout.ts
+	 *  settleGraphLayout) — read-only for everything else. */
+	readPositions(): Record<string, Position>;
+	/** Replace the whole ledger (the settle is a full-graph computation). */
+	writePositions(positions: Record<string, Position>): void;
 }
 
 // ─── JobStore — background sub-agent jobs (data/jobs) ─────────────────────────