Wave 7 close-out: the embedding ledger seam dies; notes birth via mapping lines

Part 1 — the ledger + remnants interlude (master-dispatched, owner ruling
2026-09-23: nothing configures the graph beyond chat models):

- The embedding ledger surface is gone: readEmbeddings/writeEmbeddings
  ports, the EmbeddingsLedger contract, EMBEDDINGS_FILE (config, store
  impls, graphRevision source list), and graph-deletion's vector-pruning
  step. On-disk data files stay untouched (inert history).
- The extraction embedder seam dies wholesale: ExtractionPipelineDeps
  drops the embedder dep (chat-handler + backfill/import-notes stubs go
  with it), the 'embedding' phase leaves ExtractionPhase, the usage
  capture/persist helpers die, and stages.embedding leaves
  ExtractionRunUsage (historical records keep their shape — reads are
  lenient). Extraction is two stages again, like the local-embedder era.
- Consumer-less remnants: latestQuizOutcomes + QUIZ_EVENT_KINDS,
  clusterContentId, matchClusterLabelings + Community + ClusterLabeling,
  the readClusterLabels/appendClusterLabel port seams + store impls +
  LEDGER_FILES.clusterLabels. NamingRunUsage/readNamingRuns STAY
  (standing ruling — the cost pill renders historical naming spend);
  clusterHue + MIN_CLUSTER_SIZE stay (live).
- The 'labeler' role dies: BACKGROUND_MODEL_ROLES, ROLE_SLOT, ModelRole,
  the catalog pin projections, and the UI roster strings. RolePins keys
  shrink with the union.

The notes birth fallback (owner-approved 2026-09-23, surfaced by the
interlude's live smoke: production notes imports create provenance-EMPTY
nodes (importNotes passes messages: null — the file's anchor is the
mapping line), so the provenance-only birth rule left every imported
file unclustered and invisible to the prober's session list, against the
locked file-birth ruling. A provenance-empty node now births under its
FIRST mapping line's chatId (ledger order); only notes-born nodes ever
hit the fallback (chat nodes always carry provenance; a re-encountered
node's link-append re-opens the provenance rule). Deletion-safe: mapping
lines of deleted chats are stripped alongside their provenance.

Live-verified on port 3004: a fresh notes import clusters under its
src_ id with the file path as the label, end to end with no embedder.

845/845 tests, typecheck/lint/build green.
EOF
)

src/core/layout-settle.ts

@@ -1,7 +1,6 @@
-import type { GraphEdge, GraphNode } from "./contracts.ts";
+import type { GraphEdge, GraphNode, NodeMapping, Position } from "./contracts.ts";
 import { incrementalLayout } from "./layout.ts";
 import { birthSessionPartition } from "./session-clusters.ts";
-import type { Position } from "./contracts.ts";
 
 /**
  * The merge-time settle: recompute the resting layout from the CURRENT
@@ -20,6 +19,7 @@ import type { Position } from "./contracts.ts";
 export function settleGraphLayout(graphStore: {
 	readNodes(): GraphNode[];
 	readEdges(): GraphEdge[];
+	readMappings(): NodeMapping[];
 	readPositions(): Record<string, Position>;
 	writePositions(positions: Record<string, Position>): void;
 }): void {
@@ -39,7 +39,7 @@ export function settleGraphLayout(graphStore: {
 	// core/session-clusters.ts, wave 7) — one cluster concept everywhere.
 	// The unique list is the deduped set the partition needs (lines may
 	// repeat an id — first defines).
-	const communities = birthSessionPartition(unique);
+	const communities = birthSessionPartition(unique, graphStore.readMappings());
 	const next = incrementalLayout(unique, edges, previous, { clusters: communities });
 	graphStore.writePositions(Object.fromEntries(next));
 }