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/agent/subagents/extraction.ts

@@ -16,6 +16,7 @@ import type {
 	SessionFindings,
 } from "../../core/contracts.ts";
 import { getGraph, mergeFindings, type EmissionStats, type GraphDeps } from "../../core/graph.ts";
+import { settleGraphLayout } from "../../core/layout.ts";
 import { refreshClusterLabels } from "./cluster-namer.ts";
 
 /**
@@ -714,6 +715,9 @@ export function createExtractionPipeline(deps: ExtractionPipelineDeps): Extracti
 				messages: record.messages as UIMessage[],
 				foldedAt: record.updatedAt,
 			});
+			// Option A: the layout ledger evolves with the merge (sync — the
+			// next snapshot fetch must already reflect the new nodes).
+			settleGraphLayout(graphStore);
 			persistRunUsage(chatId, Math.round(performance.now() - t0), stats);
 			console.info(
 				`[extraction ${chatId}] merged: ${stats.nodes} nodes, ${stats.edges} edges, ${stats.events} events ` +
@@ -824,6 +828,8 @@ export function createExtractionPipeline(deps: ExtractionPipelineDeps): Extracti
 			// (messages: null) — nothing to attribute, nothing to build.
 			const auditResult: AuditResult = { ...notesResult, attribution: { quiz: {} } };
 			const stats = mergeFindings(id, auditResult, { chatStore, graphStore }, { messages: null, foldedAt: input.importedAt });
+			// Option A: same post-merge settle as the chat path.
+			settleGraphLayout(graphStore);
 			persistRunUsage(id, Math.round(performance.now() - t0), stats);
 			console.info(
 				`[extraction ${id}] merged: ${stats.nodes} nodes, ${stats.edges} edges, ${stats.events} events ` +