chains-primary: stored chains replace typed edges; edges become a derived view

Owner rulings 2026-09-30: reasoning chains are the stored truth; the graph
canvas renders a lossy derived image. No migration, no backcompat — old
graph data was wiped.

- contracts: GraphChain (arg_-minted id, premises, conclusion) replaces
  typed edges; GraphEdge survives only as the untyped derived arrow;
  GraphSnapshot carries stored chains; supports edges retired entirely
- store: chains.jsonl ledger (edges.jsonl purged at load alongside legacy
  events.jsonl); readChains/appendChain seam; merge dedupes by
  (sorted premises, conclusion), re-assertions append under the same arg_ id
- core: deriveView mints implication nodes (name ⟹, statement via
  formatChainLine) plus premise→imp→conclusion arrows; clusters stay
  proposition-only (birthSessionPartition); chainsForSelection now groups
  STORED chains (chain rides iff every member selected) — independent
  arguments for one conclusion never union; chainsToGraph/chainsToEdges die
- extraction: extractor submits chains natively (expandFindings deleted);
  auditor receives propositions only; supports fan-out gone
- deletion: full death of a proposition kills every referencing chain;
  arg_-prefixed node deletes kill that chain; chainsRemoved stats
- UI: every arrow renders the ⟹ double shaft; supports toggle + thickness
  slider and detail-card edge sections deleted (card keeps name +
  proposition); chain table + practice pipeline read stored chains
- tests: 1188 green across the new seams

scripts/backfill-graph.ts

@@ -27,7 +27,7 @@ async function main() {
 			const stats = await pipeline.runExtraction(chat.id);
 			console.log(
 				`[backfill] ${chat.id} (${chat.title.slice(0, 40)}): ` +
-					`${stats.nodes} nodes, ${stats.edges} edges in ${((Date.now() - t0) / 1000).toFixed(1)}s`,
+					`${stats.nodes} nodes, ${stats.chains ?? 0} chains in ${((Date.now() - t0) / 1000).toFixed(1)}s`,
 			);
 		} catch (err) {
 			console.error(`[backfill] ${chat.id} FAILED:`, err);
@@ -35,7 +35,7 @@ async function main() {
 	}
 	const graph = getGraph(graphStore);
 	console.log(
-		`[backfill] done: ${graph.nodes.length} nodes, ${graph.edges.length} edges`,
+		`[backfill] done: ${graph.nodes.length} nodes, ${graph.chains.length} chains`,
 	);
 }
 

scripts/import-notes.ts

@@ -33,7 +33,7 @@ async function main() {
 		getChunkTokens: () => effectiveSettings().graph.extractionChunkTokens,
 	});
 	const queue = [...files];
-	const totals = { nodes: 0, edges: 0, failed: 0 };
+	const totals = { nodes: 0, chains: 0, failed: 0 };
 	const workers = Array.from({ length: Math.min(limit, files.length) }, async () => {
 		for (;;) {
 			const file = queue.shift();
@@ -43,9 +43,9 @@ async function main() {
 			try {
 				const stats = await pipeline.importNotes({ filePath, text: fs.readFileSync(filePath, "utf-8") });
 				totals.nodes += stats.nodes;
-				totals.edges += stats.edges;
+				totals.chains += stats.chains ?? 0;
 				console.log(
-					`[import-notes] ${file}: ${stats.nodes} nodes, ${stats.edges} edges in ${((Date.now() - t0) / 1000).toFixed(1)}s`,
+					`[import-notes] ${file}: ${stats.nodes} nodes, ${stats.chains ?? 0} chains in ${((Date.now() - t0) / 1000).toFixed(1)}s`,
 				);
 			} catch (err) {
 				totals.failed++;
@@ -57,8 +57,8 @@ async function main() {
 
 	const graph = getGraph(stores.graphStore);
 	console.log(
-		`[import-notes] done: +${totals.nodes} nodes, +${totals.edges} edges, ${totals.failed} failed — ` +
-			`graph now ${graph.nodes.length} nodes, ${graph.edges.length} edges`,
+		`[import-notes] done: +${totals.nodes} nodes, +${totals.chains} chains, ${totals.failed} failed — ` +
+			`graph now ${graph.nodes.length} nodes, ${graph.chains.length} chains`,
 	);
 }
 

scripts/replay-layout.ts

@@ -19,20 +19,28 @@ const depthMode: "off" | "vertical" | "radial" =
 	depthArg === "--depth=vertical" ? "vertical" : depthArg === "--depth=radial" ? "radial" : "off";
 import { incrementalLayout } from "../src/core/layout.ts";
 import { birthSessionPartition } from "../src/core/session-clusters.ts";
+import { deriveView, getGraph } from "../src/core/graph.ts";
 import type { GraphNode, Position } from "../src/core/contracts.ts";
 
 function main() {
 	const t0 = Date.now();
 
-	// Unique nodes (lines may repeat an id — first defines).
-	const seen = new Set<string>();
-	const nodes: GraphNode[] = [];
-	for (const line of graphStore.readNodes()) {
-		if (seen.has(line.id)) continue;
-		seen.add(line.id);
-		nodes.push(line);
-	}
-	const edges = graphStore.readEdges();
+	// CHAINS-PRIMARY (2026-09-30): the stored truth is nodes + chains; the
+	// replay lays out the DERIVED view (implication nodes included, untyped
+	// arrows) exactly like the real settle.
+	const graph = getGraph(graphStore);
+	const nodes = graph.nodes; // getGraph already merges lines by id
+	const view = deriveView(graph);
+	const edges = view.edges;
+	const viewNodeById = new Map(view.nodes.map((n) => [n.id, n]));
+	const chains = graph.chains;
+	// An implication node is delivered the moment its chain is complete
+	// (conclusion + every premise delivered).
+	const chainReady = (id: string): boolean => {
+		const chain = chains.find((c) => c.id === id);
+		if (!chain) return delivered.has(id);
+		return delivered.has(chain.conclusion) && chain.premises.every((p) => delivered.has(p));
+	};
 	// The cluster source (wave 7): the birth-session partition, derived on
 	// read — same as the real settle (core/layout-settle.ts).
 	const birthClusters = birthSessionPartition(nodes);
@@ -58,7 +66,7 @@ function main() {
 	const byId = new Map(nodes.map((n) => [n.id, n]));
 	const unmappedFallback = sources[sources.length - 1]?.id ?? "";
 
-	console.log(`[replay] ${nodes.length} unique nodes, ${edges.length} edge lines, ${sources.length} sources`);
+	console.log(`[replay] ${nodes.length} nodes, ${chains.length} chains, ${sources.length} sources`);
 	let maxOldShift = 0;
 	let shiftReport = "";
 	for (const source of sources) {
@@ -74,13 +82,18 @@ function main() {
 			}
 		}
 		for (const n of batch) delivered.add(n.id);
+		// Ready chains' implication nodes ride the same batch (they have no
+		// provenance of their own — the chain's completeness delivers them).
+		for (const chain of chains) {
+			if (chainReady(chain.id)) delivered.add(chain.id);
+		}
 
 		// Edges activate once BOTH endpoints exist (a later file can claim
 		// one endpoint — the edge lights up then).
 		const activeEdges = edges.filter((e) => delivered.has(e.from) && delivered.has(e.to));
 
 		const before = new Map(positions);
-		const batchNodes = nodes.filter((n) => delivered.has(n.id));
+		const batchNodes = view.nodes.filter((n) => delivered.has(n.id));
 		positions = incrementalLayout(batchNodes, activeEdges, positions, {
 			// The same partition the real settle would see for this batch:
 			// the birth-session clusters, filtered to delivered nodes.