@remnic/core 9.3.601 → 9.3.603

package/src/graph.test.ts

@@ -1,15 +1,10 @@
-import test from "node:test";
 import assert from "node:assert/strict";
+import { mkdir, mkdtemp, rm, writeFile } from "node:fs/promises";
 import os from "node:os";
 import path from "node:path";
-import { mkdir, mkdtemp, rm, writeFile } from "node:fs/promises";
+import test from "node:test";
 
-import {
-  GraphIndex,
-  graphFilePath,
-  readEdges,
-  type GraphConfig,
-} from "./graph.js";
+import { type GraphConfig, type GraphEdge, GraphIndex, graphFilePath, readEdges } from "./graph.js";
 
 function makeGraphConfig(): GraphConfig {
   return {
@@ -53,17 +48,87 @@ test("graph reads skip malformed JSON edge objects before traversal", async () =
         }),
         "",
       ].join("\n"),
-      "utf-8",
+      "utf-8"
     );
 
     const edges = await readEdges(memoryDir, "entity");
-    assert.deepEqual(edges.map((edge) => edge.to), ["c"]);
+    assert.deepEqual(
+      edges.map((edge) => edge.to),
+      ["c"]
+    );
 
     const graph = new GraphIndex(memoryDir, makeGraphConfig());
     const activated = await graph.spreadingActivation(["a"]);
-    assert.deepEqual(activated.map((candidate) => candidate.path), ["c"]);
+    assert.deepEqual(
+      activated.map((candidate) => candidate.path),
+      ["c"]
+    );
     assert.equal(Number.isFinite(activated[0]?.score), true);
   } finally {
     await rm(memoryDir, { recursive: true, force: true });
   }
 });
+
+test("spreadingActivation propagates accumulated activation from multiple seeds", async () => {
+  const memoryDir = await mkdtemp(path.join(os.tmpdir(), "remnic-graph-multi-seed-"));
+  try {
+    await writeGraphEdges(memoryDir, [
+      makeEdge("seed-a", "shared"),
+      makeEdge("seed-b", "shared"),
+      makeEdge("shared", "downstream"),
+    ]);
+
+    const graph = new GraphIndex(memoryDir, makeGraphConfig());
+    const activated = await graph.spreadingActivation(["seed-a", "seed-b"]);
+    const scores = new Map(activated.map((candidate) => [candidate.path, candidate.score]));
+
+    assert.equal(scores.get("shared"), 1);
+    assert.equal(scores.get("downstream"), 0.5);
+  } finally {
+    await rm(memoryDir, { recursive: true, force: true });
+  }
+});
+
+test("spreadingActivation propagates same-depth alternate path activation", async () => {
+  const memoryDir = await mkdtemp(path.join(os.tmpdir(), "remnic-graph-alt-path-"));
+  try {
+    await writeGraphEdges(memoryDir, [
+      makeEdge("seed", "left"),
+      makeEdge("seed", "right"),
+      makeEdge("left", "shared"),
+      makeEdge("right", "shared"),
+      makeEdge("shared", "downstream"),
+    ]);
+
+    const graph = new GraphIndex(memoryDir, {
+      ...makeGraphConfig(),
+      maxGraphTraversalSteps: 3,
+    });
+    const activated = await graph.spreadingActivation(["seed"]);
+    const scores = new Map(activated.map((candidate) => [candidate.path, candidate.score]));
+
+    assert.equal(scores.get("left"), 0.5);
+    assert.equal(scores.get("right"), 0.5);
+    assert.equal(scores.get("shared"), 0.5);
+    assert.equal(scores.get("downstream"), 0.25);
+  } finally {
+    await rm(memoryDir, { recursive: true, force: true });
+  }
+});
+
+function makeEdge(from: string, to: string): GraphEdge {
+  return {
+    from,
+    to,
+    type: "entity",
+    weight: 1,
+    label: "test",
+    ts: "2026-01-01T00:00:00.000Z",
+  };
+}
+
+async function writeGraphEdges(memoryDir: string, edges: GraphEdge[]): Promise<void> {
+  const filePath = graphFilePath(memoryDir, "entity");
+  await mkdir(path.dirname(filePath), { recursive: true });
+  await writeFile(filePath, `${edges.map((edge) => JSON.stringify(edge)).join("\n")}\n`, "utf-8");
+}

package/src/graph.ts

@@ -10,8 +10,8 @@
  * All writes are fail-open: errors are caught/logged, never thrown.
  */
 
-import { mkdir, appendFile, readFile } from "node:fs/promises";
-import * as path from "path";
+import { appendFile, mkdir, readFile } from "node:fs/promises";
+import * as path from "node:path";
 
 import { readEdgeConfidence } from "./graph-edge-reinforcement.js";
 import { emitGraphEvent } from "./graph-events.js";
@@ -66,14 +66,7 @@ export const DEFAULT_GRAPH_TRAVERSAL_CONFIDENCE_FLOOR = 0.2;
 export const DEFAULT_GRAPH_TRAVERSAL_PAGERANK_ITERATIONS = 8;
 
 // Causal signal phrases — order matters (most specific first)
-export const CAUSAL_PHRASES = [
-  "as a result",
-  "led to",
-  "because of",
-  "therefore",
-  "caused",
-  "because",
-];
+export const CAUSAL_PHRASES = ["as a result", "led to", "because of", "therefore", "caused", "because"];
 
 export function graphsDir(memoryDir: string): string {
   return path.join(memoryDir, "state", "graphs");
@@ -114,8 +107,8 @@ export function withGraphWriteLock<T>(filePath: string, fn: () => Promise<T>): P
     filePath,
     next.then(
       () => undefined,
-      () => undefined,
-    ),
+      () => undefined
+    )
   );
   return next;
 }
@@ -123,7 +116,7 @@ export function withGraphWriteLock<T>(filePath: string, fn: () => Promise<T>): P
 export async function appendEdge(memoryDir: string, edge: GraphEdge): Promise<void> {
   await ensureGraphsDir(memoryDir);
   const filePath = graphFilePath(memoryDir, edge.type);
-  const line = JSON.stringify(edge) + "\n";
+  const line = `${JSON.stringify(edge)}\n`;
   await withGraphWriteLock(filePath, async () => {
     await appendFile(filePath, line, "utf8");
   });
@@ -205,7 +198,7 @@ export async function readEdgesStrict(memoryDir: string, type: GraphType): Promi
  */
 export async function readAllEdges(
   memoryDir: string,
-  config: Pick<GraphConfig, "entityGraphEnabled" | "timeGraphEnabled" | "causalGraphEnabled">,
+  config: Pick<GraphConfig, "entityGraphEnabled" | "timeGraphEnabled" | "causalGraphEnabled">
 ): Promise<GraphEdge[]> {
   const parts: GraphEdge[][] = await Promise.all([
     config.entityGraphEnabled ? readEdges(memoryDir, "entity") : Promise.resolve([]),
@@ -243,9 +236,12 @@ function isValidGraphEdge(raw: unknown, expectedType: GraphType): raw is GraphEd
   const edge = raw as Record<string, unknown>;
   return (
     edge.type === expectedType &&
-    typeof edge.from === "string" && edge.from.length > 0 &&
-    typeof edge.to === "string" && edge.to.length > 0 &&
-    typeof edge.weight === "number" && Number.isFinite(edge.weight) &&
+    typeof edge.from === "string" &&
+    edge.from.length > 0 &&
+    typeof edge.to === "string" &&
+    edge.to.length > 0 &&
+    typeof edge.weight === "number" &&
+    Number.isFinite(edge.weight) &&
     typeof edge.label === "string" &&
     typeof edge.ts === "string"
   );
@@ -258,7 +254,7 @@ export async function analyzeGraphHealth(
     timeGraphEnabled?: boolean;
     causalGraphEnabled?: boolean;
     includeRepairGuidance?: boolean;
-  },
+  }
 ): Promise<GraphHealthReport> {
   const enabledTypes: GraphType[] = [];
   if (options?.entityGraphEnabled !== false) enabledTypes.push("entity");
@@ -324,7 +320,7 @@ export async function analyzeGraphHealth(
       validEdges: 0,
       corruptLines: 0,
       uniqueNodes: globalNodes.size,
-    },
+    }
   );
   totals.uniqueNodes = globalNodes.size;
 
@@ -338,10 +334,14 @@ export async function analyzeGraphHealth(
   if (options?.includeRepairGuidance === true) {
     const guidance: string[] = [];
     if (totals.corruptLines > 0) {
-      guidance.push("Corrupt graph lines detected: back up memory/state/graphs, then rebuild graphs from clean memory replay/extraction runs.");
+      guidance.push(
+        "Corrupt graph lines detected: back up memory/state/graphs, then rebuild graphs from clean memory replay/extraction runs."
+      );
     }
     if (totals.validEdges === 0) {
-      guidance.push("No valid edges detected yet: run normal extraction traffic (or replay ingestion) to seed graph files.");
+      guidance.push(
+        "No valid edges detected yet: run normal extraction traffic (or replay ingestion) to seed graph files."
+      );
     }
     if (guidance.length > 0) report.repairGuidance = guidance;
   }
@@ -392,10 +392,7 @@ export class GraphIndex {
   }
 
   private async loadEdgesCached(): Promise<GraphEdge[]> {
-    if (
-      this.edgeCache &&
-      Date.now() - this.edgeCache.loadedAt < GraphIndex.EDGE_CACHE_TTL_MS
-    ) {
+    if (this.edgeCache && Date.now() - this.edgeCache.loadedAt < GraphIndex.EDGE_CACHE_TTL_MS) {
       return this.edgeCache.allEdges;
     }
     const allEdges = await readAllEdges(this.memoryDir, {
@@ -520,21 +517,23 @@ export class GraphIndex {
        * Default `false` (floor from config is applied).
        */
       includeLowConfidence?: boolean;
-    },
-  ): Promise<Array<{
-    path: string;
-    score: number;
-    seed: string;
-    hopDepth: number;
-    decayedWeight: number;
-    graphType: "entity" | "time" | "causal";
-    /**
-     * Confidence of the edge that produced this candidate's recorded
-     * provenance (the strongest edge along the chosen entry path).
-     * In `[0, 1]`. Legacy edges without `confidence` surface as 1.0.
-     */
-    edgeConfidence: number;
-  }>> {
+    }
+  ): Promise<
+    Array<{
+      path: string;
+      score: number;
+      seed: string;
+      hopDepth: number;
+      decayedWeight: number;
+      graphType: "entity" | "time" | "causal";
+      /**
+       * Confidence of the edge that produced this candidate's recorded
+       * provenance (the strongest edge along the chosen entry path).
+       * In `[0, 1]`. Legacy edges without `confidence` surface as 1.0.
+       */
+      edgeConfidence: number;
+    }>
+  > {
     if (!this.cfg.multiGraphMemoryEnabled) return [];
     const steps = maxSteps ?? this.cfg.maxGraphTraversalSteps;
     const decay = this.cfg.graphActivationDecay;
@@ -543,12 +542,9 @@ export class GraphIndex {
     // Otherwise clamp the configured floor into [0, 1] so misconfiguration
     // cannot (a) admit edges with negative confidence or (b) reject every
     // edge.
-    const floor = opts?.includeLowConfidence === true
-      ? 0
-      : clampConfidenceFloor(this.cfg.graphTraversalConfidenceFloor);
-    const iterations = clampPageRankIterations(
-      this.cfg.graphTraversalPageRankIterations,
-    );
+    const floor =
+      opts?.includeLowConfidence === true ? 0 : clampConfidenceFloor(this.cfg.graphTraversalConfidenceFloor);
+    const iterations = clampPageRankIterations(this.cfg.graphTraversalPageRankIterations);
 
     try {
       const allEdges = await this.loadEdgesCached();
@@ -581,50 +577,67 @@ export class GraphIndex {
           edgeConfidence: number;
         }
       >();
-      const visited = new Set<string>(seeds);
-
-      // BFS queue: [nodePath, hop, seedPath]
-      const queue: Array<[string, number, string]> = seeds.map((s) => [s, 0, s]);
-
-      while (queue.length > 0) {
-        const [node, hop, sourceSeed] = queue.shift()!;
-        if (hop >= steps) continue;
-
-        const edges = adj.get(node) ?? [];
-        for (const edge of edges) {
-          const neighbor = edge.to === node ? edge.from : edge.to;
-          const conf = readEdgeConfidence(edge);
-          // Defense in depth: the adjacency build already drops sub-floor
-          // edges, but if a synthesized reverse edge ever bypassed that
-          // path, this guard keeps spreading activation honest.
-          if (conf < floor) continue;
-          const score = edge.weight * conf * Math.pow(decay, hop + 1);
-
-          if (!seedSet.has(neighbor)) {
-            const existing = scores.get(neighbor) ?? 0;
-            scores.set(neighbor, existing + score);
-
-            const prev = provenance.get(neighbor);
-            if (
-              !prev ||
-              hop + 1 < prev.hopDepth ||
-              (hop + 1 === prev.hopDepth && score > prev.decayedWeight)
-            ) {
-              provenance.set(neighbor, {
-                seed: sourceSeed,
-                hopDepth: hop + 1,
-                decayedWeight: score,
-                graphType: edge.type,
-                edgeConfidence: conf,
-              });
+      let frontier = new Map<string, { node: string; seed: string; activation: number }>();
+      const reachedBySeed = new Map<string, Set<string>>();
+      for (const seed of seeds) {
+        frontier.set(`${seed}\0${seed}`, { node: seed, seed, activation: 1 });
+        reachedBySeed.set(seed, new Set([seed]));
+      }
+
+      for (let hop = 0; hop < steps && frontier.size > 0; hop++) {
+        const nextFrontier = new Map<string, { node: string; seed: string; activation: number }>();
+
+        for (const { node, seed: sourceSeed, activation } of frontier.values()) {
+          const edges = adj.get(node) ?? [];
+          for (const edge of edges) {
+            const neighbor = edge.to === node ? edge.from : edge.to;
+            const conf = readEdgeConfidence(edge);
+            // Defense in depth: the adjacency build already drops sub-floor
+            // edges, but if a synthesized reverse edge ever bypassed that
+            // path, this guard keeps spreading activation honest.
+            if (conf < floor) continue;
+            const score = activation * edge.weight * conf * decay;
+            const reachedForSeed = reachedBySeed.get(sourceSeed);
+            if (reachedForSeed?.has(neighbor)) {
+              continue;
             }
-          }
 
-          if (!visited.has(neighbor)) {
-            visited.add(neighbor);
-            queue.push([neighbor, hop + 1, sourceSeed]);
+            if (!seedSet.has(neighbor)) {
+              const existing = scores.get(neighbor) ?? 0;
+              scores.set(neighbor, existing + score);
+
+              const prev = provenance.get(neighbor);
+              if (!prev || hop + 1 < prev.hopDepth || (hop + 1 === prev.hopDepth && score > prev.decayedWeight)) {
+                provenance.set(neighbor, {
+                  seed: sourceSeed,
+                  hopDepth: hop + 1,
+                  decayedWeight: score,
+                  graphType: edge.type,
+                  edgeConfidence: conf,
+                });
+              }
+
+              if (hop + 1 < steps) {
+                const frontierKey = `${sourceSeed}\0${neighbor}`;
+                const existingFrontier = nextFrontier.get(frontierKey);
+                if (existingFrontier) {
+                  existingFrontier.activation += score;
+                } else {
+                  nextFrontier.set(frontierKey, {
+                    node: neighbor,
+                    seed: sourceSeed,
+                    activation: score,
+                  });
+                }
+              }
+            }
           }
         }
+
+        for (const { node, seed } of nextFrontier.values()) {
+          reachedBySeed.get(seed)?.add(node);
+        }
+        frontier = nextFrontier;
       }
 
       // Issue #681 PR 3/3 — optional PageRank-style refinement.
@@ -712,7 +725,7 @@ export function clampPageRankIterations(raw: unknown): number {
 export function applyPageRankRefinement(
   scores: Map<string, number>,
   adj: Map<string, GraphEdge[]>,
-  opts: { iterations: number; floor: number; damping: number },
+  opts: { iterations: number; floor: number; damping: number }
 ): void {
   const { iterations, floor, damping } = opts;
   if (iterations <= 0 || scores.size === 0) return;
@@ -793,7 +806,7 @@ export function applyPageRankRefinement(
  */
 export function applyLateralInhibition(
   scores: Map<string, number>,
-  opts: { beta: number; topM: number },
+  opts: { beta: number; topM: number }
 ): Map<string, number> {
   const { beta, topM } = opts;
   if (beta === 0 || topM === 0) return new Map(scores);

package/dist/chunk-4JRRISLU.js.map

@@ -1 +0,0 @@
-{"version":3,"sources":["../src/graph.ts"],"sourcesContent":["/**\n * Multi-Graph Memory (MAGMA/SYNAPSE-inspired, v8.2)\n *\n * Maintains three typed edge graphs:\n *   entity.jsonl  — memories sharing a named entity (entityRef)\n *   time.jsonl    — consecutive memories in the same thread/session\n *   causal.jsonl  — memories linked by causal language heuristics\n *\n * Stored under `<memoryDir>/state/graphs/`.\n * All writes are fail-open: errors are caught/logged, never thrown.\n */\n\nimport { mkdir, appendFile, readFile } from \"node:fs/promises\";\nimport * as path from \"path\";\n\nimport { readEdgeConfidence } from \"./graph-edge-reinforcement.js\";\nimport { emitGraphEvent } from \"./graph-events.js\";\n\nexport type GraphType = \"entity\" | \"time\" | \"causal\";\n\nexport interface GraphEdge {\n  from: string; // relative memory path (e.g. \"facts/2026-02-22/abc.md\")\n  to: string; // relative memory path\n  type: GraphType;\n  weight: number; // 1.0 default, decay applied during traversal\n  label: string; // entity name, threadId, or matched causal phrase\n  ts: string; // ISO timestamp of edge creation\n\n  // Issue #681 — edge confidence + reinforcement (PR 1/3: schema + primitive only).\n  // Both fields are optional so existing edges without confidence still validate.\n  // Treat a missing `confidence` as 1.0 (legacy behavior) at read sites.\n  // PR 2/3 wires the maintenance decay job; PR 3/3 weights PageRank traversal by confidence.\n  confidence?: number; // [0, 1]; missing = 1.0\n  lastReinforcedAt?: string; // ISO timestamp of most recent reinforcement\n}\n\nexport interface GraphConfig {\n  multiGraphMemoryEnabled: boolean;\n  entityGraphEnabled: boolean;\n  timeGraphEnabled: boolean;\n  causalGraphEnabled: boolean;\n  maxGraphTraversalSteps: number;\n  graphActivationDecay: number;\n  maxEntityGraphEdgesPerMemory: number;\n  graphLateralInhibitionEnabled: boolean;\n  graphLateralInhibitionBeta: number;\n  graphLateralInhibitionTopM: number;\n  /**\n   * Issue #681 PR 3/3 — minimum edge confidence required for traversal.\n   * Edges with confidence below this floor are pruned. Legacy edges\n   * (no `confidence` field) are treated as 1.0 and always pass.\n   * Range `[0, 1]`. Default 0.2.\n   */\n  graphTraversalConfidenceFloor: number;\n  /**\n   * Issue #681 PR 3/3 — number of PageRank-style refinement iterations\n   * applied on top of BFS activation. Set to 0 to disable refinement\n   * and return raw BFS scores. Default 8.\n   */\n  graphTraversalPageRankIterations: number;\n}\n\n/** Default minimum edge confidence required for traversal (issue #681 PR 3/3). */\nexport const DEFAULT_GRAPH_TRAVERSAL_CONFIDENCE_FLOOR = 0.2;\n/** Default PageRank-style refinement iteration count (issue #681 PR 3/3). */\nexport const DEFAULT_GRAPH_TRAVERSAL_PAGERANK_ITERATIONS = 8;\n\n// Causal signal phrases — order matters (most specific first)\nexport const CAUSAL_PHRASES = [\n  \"as a result\",\n  \"led to\",\n  \"because of\",\n  \"therefore\",\n  \"caused\",\n  \"because\",\n];\n\nexport function graphsDir(memoryDir: string): string {\n  return path.join(memoryDir, \"state\", \"graphs\");\n}\n\nexport function graphFilePath(memoryDir: string, type: GraphType): string {\n  return path.join(graphsDir(memoryDir), `${type}.jsonl`);\n}\n\nexport async function ensureGraphsDir(memoryDir: string): Promise<void> {\n  await mkdir(graphsDir(memoryDir), { recursive: true });\n}\n\n// ---------------------------------------------------------------------------\n// Per-graph-file write lock (gotcha #40 promise-chain pattern).\n//\n// Both the append path (`appendEdge`) and the rewrite path used by the\n// decay maintenance job must serialize on the same lock keyed by the\n// JSONL file path. Without this, an extraction can append a new edge\n// between the decay job's read-snapshot and rewrite, silently dropping\n// the appended edge during active traffic (issue #729 / Codex P1).\n// ---------------------------------------------------------------------------\nconst graphWriteLocks = new Map<string, Promise<void>>();\n\n/**\n * Run `fn` while holding the write lock for the given graph JSONL file.\n *\n * The lock is keyed by absolute file path so concurrent writes to\n * different graph types proceed independently. The chain recovers from\n * rejection (gotcha #40) so a single I/O failure does not poison all\n * future writers, but the original error is still surfaced to the\n * caller of `withGraphWriteLock`.\n */\nexport function withGraphWriteLock<T>(filePath: string, fn: () => Promise<T>): Promise<T> {\n  const prev = graphWriteLocks.get(filePath) ?? Promise.resolve();\n  const next = prev.then(fn, fn);\n  graphWriteLocks.set(\n    filePath,\n    next.then(\n      () => undefined,\n      () => undefined,\n    ),\n  );\n  return next;\n}\n\nexport async function appendEdge(memoryDir: string, edge: GraphEdge): Promise<void> {\n  await ensureGraphsDir(memoryDir);\n  const filePath = graphFilePath(memoryDir, edge.type);\n  const line = JSON.stringify(edge) + \"\\n\";\n  await withGraphWriteLock(filePath, async () => {\n    await appendFile(filePath, line, \"utf8\");\n  });\n  // Emit edge-added event for SSE subscribers (issue #691 PR 5/5).\n  // Fail-open: emitGraphEvent catches listener errors so a bad SSE client\n  // can never surface into the extraction pipeline.\n  emitGraphEvent(memoryDir, \"edge-added\", {\n    source: edge.from,\n    target: edge.to,\n    kind: edge.type,\n    weight: edge.weight,\n    label: edge.label,\n    confidence: typeof edge.confidence === \"number\" ? edge.confidence : 1.0,\n  });\n}\n\nfunction isNodeError(err: unknown): err is NodeJS.ErrnoException {\n  return typeof err === \"object\" && err !== null && \"code\" in err;\n}\n\nfunction parseEdgesJsonl(raw: string, expectedType: GraphType): GraphEdge[] {\n  const edges: GraphEdge[] = [];\n  for (const line of raw.split(\"\\n\")) {\n    const trimmed = line.trim();\n    if (!trimmed) continue;\n    try {\n      const parsed = JSON.parse(trimmed) as unknown;\n      if (isValidGraphEdge(parsed, expectedType)) {\n        edges.push(parsed);\n      }\n    } catch {\n      // skip corrupt lines — fail-open for partial JSONL recovery\n    }\n  }\n  return edges;\n}\n\n/**\n * Read all edges of a given type from the JSONL file.\n * Returns [] if the file doesn't exist or any read error occurs (fail-open).\n *\n * Production traversal callers (recall/PageRank) depend on this fail-open\n * posture so a temporarily missing or unreadable graph file never blocks\n * a recall. Maintenance jobs that need to distinguish ENOENT from real\n * I/O failures must use {@link readEdgesStrict} instead.\n */\nexport async function readEdges(memoryDir: string, type: GraphType): Promise<GraphEdge[]> {\n  const filePath = graphFilePath(memoryDir, type);\n  try {\n    const raw = await readFile(filePath, \"utf8\");\n    return parseEdgesJsonl(raw, type);\n  } catch {\n    return [];\n  }\n}\n\n/**\n * Same as {@link readEdges} but only swallows `ENOENT`; all other read\n * errors (`EACCES`, `EIO`, …) are propagated. Used by the graph-edge\n * decay maintenance job so I/O outages surface as a failed run instead\n * of being silently reported as \"no edges to decay\" (issue #729 /\n * Codex P1, line 120).\n */\nexport async function readEdgesStrict(memoryDir: string, type: GraphType): Promise<GraphEdge[]> {\n  const filePath = graphFilePath(memoryDir, type);\n  try {\n    const raw = await readFile(filePath, \"utf8\");\n    return parseEdgesJsonl(raw, type);\n  } catch (err) {\n    if (isNodeError(err) && err.code === \"ENOENT\") {\n      return [];\n    }\n    throw err;\n  }\n}\n\n/**\n * Read edges from all enabled graph types.\n */\nexport async function readAllEdges(\n  memoryDir: string,\n  config: Pick<GraphConfig, \"entityGraphEnabled\" | \"timeGraphEnabled\" | \"causalGraphEnabled\">,\n): Promise<GraphEdge[]> {\n  const parts: GraphEdge[][] = await Promise.all([\n    config.entityGraphEnabled ? readEdges(memoryDir, \"entity\") : Promise.resolve([]),\n    config.timeGraphEnabled ? readEdges(memoryDir, \"time\") : Promise.resolve([]),\n    config.causalGraphEnabled ? readEdges(memoryDir, \"causal\") : Promise.resolve([]),\n  ]);\n  return parts.flat();\n}\n\nexport interface GraphHealthFileStats {\n  type: GraphType;\n  filePath: string;\n  exists: boolean;\n  totalLines: number;\n  validEdges: number;\n  corruptLines: number;\n  uniqueNodes: number;\n}\n\nexport interface GraphHealthReport {\n  generatedAt: string;\n  enabledTypes: GraphType[];\n  totals: {\n    totalLines: number;\n    validEdges: number;\n    corruptLines: number;\n    uniqueNodes: number;\n  };\n  files: GraphHealthFileStats[];\n  repairGuidance?: string[];\n}\n\nfunction isValidGraphEdge(raw: unknown, expectedType: GraphType): raw is GraphEdge {\n  if (!raw || typeof raw !== \"object\") return false;\n  const edge = raw as Record<string, unknown>;\n  return (\n    edge.type === expectedType &&\n    typeof edge.from === \"string\" && edge.from.length > 0 &&\n    typeof edge.to === \"string\" && edge.to.length > 0 &&\n    typeof edge.weight === \"number\" && Number.isFinite(edge.weight) &&\n    typeof edge.label === \"string\" &&\n    typeof edge.ts === \"string\"\n  );\n}\n\nexport async function analyzeGraphHealth(\n  memoryDir: string,\n  options?: {\n    entityGraphEnabled?: boolean;\n    timeGraphEnabled?: boolean;\n    causalGraphEnabled?: boolean;\n    includeRepairGuidance?: boolean;\n  },\n): Promise<GraphHealthReport> {\n  const enabledTypes: GraphType[] = [];\n  if (options?.entityGraphEnabled !== false) enabledTypes.push(\"entity\");\n  if (options?.timeGraphEnabled !== false) enabledTypes.push(\"time\");\n  if (options?.causalGraphEnabled !== false) enabledTypes.push(\"causal\");\n\n  const files: GraphHealthFileStats[] = [];\n  const globalNodes = new Set<string>();\n\n  for (const type of enabledTypes) {\n    const filePath = graphFilePath(memoryDir, type);\n    let exists = true;\n    let totalLines = 0;\n    let validEdges = 0;\n    let corruptLines = 0;\n    const nodes = new Set<string>();\n\n    try {\n      const raw = await readFile(filePath, \"utf8\");\n      for (const line of raw.split(\"\\n\")) {\n        const trimmed = line.trim();\n        if (!trimmed) continue;\n        totalLines += 1;\n        try {\n          const parsed = JSON.parse(trimmed) as unknown;\n          if (!isValidGraphEdge(parsed, type)) {\n            corruptLines += 1;\n            continue;\n          }\n          validEdges += 1;\n          nodes.add(parsed.from);\n          nodes.add(parsed.to);\n          globalNodes.add(parsed.from);\n          globalNodes.add(parsed.to);\n        } catch {\n          corruptLines += 1;\n        }\n      }\n    } catch {\n      exists = false;\n    }\n\n    files.push({\n      type,\n      filePath,\n      exists,\n      totalLines,\n      validEdges,\n      corruptLines,\n      uniqueNodes: nodes.size,\n    });\n  }\n\n  const totals = files.reduce(\n    (acc, item) => {\n      acc.totalLines += item.totalLines;\n      acc.validEdges += item.validEdges;\n      acc.corruptLines += item.corruptLines;\n      return acc;\n    },\n    {\n      totalLines: 0,\n      validEdges: 0,\n      corruptLines: 0,\n      uniqueNodes: globalNodes.size,\n    },\n  );\n  totals.uniqueNodes = globalNodes.size;\n\n  const report: GraphHealthReport = {\n    generatedAt: new Date().toISOString(),\n    enabledTypes,\n    totals,\n    files,\n  };\n\n  if (options?.includeRepairGuidance === true) {\n    const guidance: string[] = [];\n    if (totals.corruptLines > 0) {\n      guidance.push(\"Corrupt graph lines detected: back up memory/state/graphs, then rebuild graphs from clean memory replay/extraction runs.\");\n    }\n    if (totals.validEdges === 0) {\n      guidance.push(\"No valid edges detected yet: run normal extraction traffic (or replay ingestion) to seed graph files.\");\n    }\n    if (guidance.length > 0) report.repairGuidance = guidance;\n  }\n\n  return report;\n}\n\n/**\n * Detect causal signal phrases in text. Returns the first matched phrase, or null.\n */\nexport function detectCausalPhrase(text: string): string | null {\n  const lower = text.toLowerCase();\n  for (const phrase of CAUSAL_PHRASES) {\n    if (lower.includes(phrase)) return phrase;\n  }\n  return null;\n}\n\n/**\n * GraphIndex — builds and updates the three memory graphs.\n *\n * Usage (orchestrator):\n *   this.graphIndex = new GraphIndex(config.memoryDir, config);\n *\n *   // After each memory write:\n *   await this.graphIndex.onMemoryWritten(memoryPath, frontmatter, threadId, recentInThread);\n */\nexport class GraphIndex {\n  private readonly memoryDir: string;\n  private readonly cfg: GraphConfig;\n\n  // Cache for readAllEdges() result.  With 30k+ entity edges (6 MB JSONL) the\n  // file read + JSON parse takes 2-4 s per call.  This instance-level cache\n  // eliminates that overhead on every spreadingActivation() call; it is\n  // invalidated (set to null) in onMemoryWritten() so new edges appear promptly.\n  private edgeCache: { allEdges: GraphEdge[]; loadedAt: number } | null = null;\n  private static readonly EDGE_CACHE_TTL_MS = 300_000; // 5 minutes\n\n  constructor(memoryDir: string, cfg: GraphConfig) {\n    this.memoryDir = memoryDir;\n    this.cfg = cfg;\n  }\n\n  /** Clear the edge cache so the next spreadingActivation() re-reads from disk.\n   *  Call after any code path that appends edges outside of onMemoryWritten(). */\n  invalidateEdgeCache(): void {\n    this.edgeCache = null;\n  }\n\n  private async loadEdgesCached(): Promise<GraphEdge[]> {\n    if (\n      this.edgeCache &&\n      Date.now() - this.edgeCache.loadedAt < GraphIndex.EDGE_CACHE_TTL_MS\n    ) {\n      return this.edgeCache.allEdges;\n    }\n    const allEdges = await readAllEdges(this.memoryDir, {\n      entityGraphEnabled: this.cfg.entityGraphEnabled,\n      timeGraphEnabled: this.cfg.timeGraphEnabled,\n      causalGraphEnabled: this.cfg.causalGraphEnabled,\n    });\n    this.edgeCache = { allEdges, loadedAt: Date.now() };\n    return allEdges;\n  }\n\n  /**\n   * Called after a memory is written to disk.\n   *\n   * @param memoryPath - relative path from memoryDir (e.g. \"facts/2026-02-22/abc.md\")\n   * @param entityRef  - entityRef frontmatter field (if any)\n   * @param content    - full memory text (for causal detection)\n   * @param created    - ISO timestamp of this memory\n   * @param threadId   - current thread ID (for time graph)\n   * @param recentInThread - paths of the N most-recent memories in this thread (for time graph)\n   * @param entitySiblings - paths of other memories that share the same entityRef (for entity graph)\n   */\n  async onMemoryWritten(opts: {\n    memoryPath: string;\n    entityRef?: string;\n    content: string;\n    created: string;\n    threadId?: string;\n    recentInThread?: string[];\n    entitySiblings?: string[];\n    causalPredecessor?: string;\n  }): Promise<void> {\n    if (!this.cfg.multiGraphMemoryEnabled) return;\n    const ts = new Date().toISOString();\n\n    try {\n      // Entity graph\n      if (this.cfg.entityGraphEnabled && opts.entityRef && opts.entitySiblings?.length) {\n        const siblings = opts.entitySiblings.slice(0, this.cfg.maxEntityGraphEdgesPerMemory);\n        for (const sibling of siblings) {\n          await appendEdge(this.memoryDir, {\n            from: opts.memoryPath,\n            to: sibling,\n            type: \"entity\",\n            weight: 1.0,\n            label: opts.entityRef,\n            ts,\n          });\n        }\n      }\n\n      // Time graph — link to most recent memory in same thread\n      if (this.cfg.timeGraphEnabled && opts.threadId && opts.recentInThread?.length) {\n        const predecessor = opts.recentInThread[opts.recentInThread.length - 1];\n        if (predecessor && predecessor !== opts.memoryPath) {\n          await appendEdge(this.memoryDir, {\n            from: predecessor,\n            to: opts.memoryPath,\n            type: \"time\",\n            weight: 1.0,\n            label: opts.threadId,\n            ts,\n          });\n        }\n      }\n\n      // Causal graph\n      if (this.cfg.causalGraphEnabled && opts.causalPredecessor) {\n        const phrase = detectCausalPhrase(opts.content);\n        if (phrase) {\n          await appendEdge(this.memoryDir, {\n            from: opts.causalPredecessor,\n            to: opts.memoryPath,\n            type: \"causal\",\n            weight: 1.0,\n            label: phrase,\n            ts,\n          });\n        }\n      }\n    } catch (err) {\n      // Fail-open: graph write errors must never surface to caller\n      const { log } = await import(\"./logger.js\");\n      log.warn(`[graph] onMemoryWritten error: ${err}`);\n    } finally {\n      // Invalidate edge cache so spreadingActivation() picks up new edges.\n      // In `finally` so the cache is cleared even on partial write failure.\n      this.edgeCache = null;\n    }\n  }\n\n  /**\n   * Spreading activation BFS (SYNAPSE-inspired).\n   *\n   * Starting from `seeds`, traverse the combined graph for up to `maxSteps` hops.\n   * Each candidate gets an activation score = edge.weight × edgeConfidence × decay^hop.\n   *\n   * Issue #681 PR 3/3 — confidence-aware traversal:\n   *   - Each edge's `weight` is multiplied by its `confidence` (legacy edges\n   *     missing `confidence` are treated as 1.0, preserving prior behavior).\n   *   - Edges with `confidence < graphTraversalConfidenceFloor` are pruned and\n   *     contribute neither activation nor downstream neighbors.\n   *   - When `graphTraversalPageRankIterations > 0`, an additional PageRank-\n   *     style refinement pass redistributes activation along confidence-weighted\n   *     edges, sharpening the ranking among multi-hop candidates.\n   *   - Per-result provenance includes the highest-confidence edge that landed\n   *     on each candidate, so the X-ray surface can attribute pruning and\n   *     ranking decisions back to specific edges.\n   *\n   * @param seeds    - initial memory paths to expand from (e.g. QMD top results)\n   * @param maxSteps - max BFS hops (from config: maxGraphTraversalSteps)\n   * @returns Array of {path, score, edgeConfidence, ...} sorted descending, not including seed paths\n   */\n  async spreadingActivation(\n    seeds: string[],\n    maxSteps?: number,\n    opts?: {\n      /**\n       * Issue #681 — when `true`, bypasses the configured\n       * `graphTraversalConfidenceFloor` and includes low-confidence\n       * edges in traversal.  Equivalent to forcing the floor to `0`.\n       * Default `false` (floor from config is applied).\n       */\n      includeLowConfidence?: boolean;\n    },\n  ): Promise<Array<{\n    path: string;\n    score: number;\n    seed: string;\n    hopDepth: number;\n    decayedWeight: number;\n    graphType: \"entity\" | \"time\" | \"causal\";\n    /**\n     * Confidence of the edge that produced this candidate's recorded\n     * provenance (the strongest edge along the chosen entry path).\n     * In `[0, 1]`. Legacy edges without `confidence` surface as 1.0.\n     */\n    edgeConfidence: number;\n  }>> {\n    if (!this.cfg.multiGraphMemoryEnabled) return [];\n    const steps = maxSteps ?? this.cfg.maxGraphTraversalSteps;\n    const decay = this.cfg.graphActivationDecay;\n    // When `includeLowConfidence` is set, use floor=0 so all edges\n    // participate in traversal regardless of their decay state.\n    // Otherwise clamp the configured floor into [0, 1] so misconfiguration\n    // cannot (a) admit edges with negative confidence or (b) reject every\n    // edge.\n    const floor = opts?.includeLowConfidence === true\n      ? 0\n      : clampConfidenceFloor(this.cfg.graphTraversalConfidenceFloor);\n    const iterations = clampPageRankIterations(\n      this.cfg.graphTraversalPageRankIterations,\n    );\n\n    try {\n      const allEdges = await this.loadEdgesCached();\n\n      // Build adjacency index: from → edges, to → edges (bidirectional for entity/time, directional for causal).\n      // Edges below the confidence floor are pruned at index time so neither\n      // direct activation nor downstream BFS expansion can re-introduce them.\n      const adj = new Map<string, GraphEdge[]>();\n      for (const edge of allEdges) {\n        const conf = readEdgeConfidence(edge);\n        if (conf < floor) continue;\n        if (!adj.has(edge.from)) adj.set(edge.from, []);\n        adj.get(edge.from)!.push(edge);\n        // Entity and time edges are bidirectional\n        if (edge.type !== \"causal\") {\n          if (!adj.has(edge.to)) adj.set(edge.to, []);\n          adj.get(edge.to)!.push({ ...edge, from: edge.to, to: edge.from });\n        }\n      }\n\n      const seedSet = new Set(seeds);\n      const scores = new Map<string, number>(); // candidate path → accumulated activation score\n      const provenance = new Map<\n        string,\n        {\n          seed: string;\n          hopDepth: number;\n          decayedWeight: number;\n          graphType: \"entity\" | \"time\" | \"causal\";\n          edgeConfidence: number;\n        }\n      >();\n      const visited = new Set<string>(seeds);\n\n      // BFS queue: [nodePath, hop, seedPath]\n      const queue: Array<[string, number, string]> = seeds.map((s) => [s, 0, s]);\n\n      while (queue.length > 0) {\n        const [node, hop, sourceSeed] = queue.shift()!;\n        if (hop >= steps) continue;\n\n        const edges = adj.get(node) ?? [];\n        for (const edge of edges) {\n          const neighbor = edge.to === node ? edge.from : edge.to;\n          const conf = readEdgeConfidence(edge);\n          // Defense in depth: the adjacency build already drops sub-floor\n          // edges, but if a synthesized reverse edge ever bypassed that\n          // path, this guard keeps spreading activation honest.\n          if (conf < floor) continue;\n          const score = edge.weight * conf * Math.pow(decay, hop + 1);\n\n          if (!seedSet.has(neighbor)) {\n            const existing = scores.get(neighbor) ?? 0;\n            scores.set(neighbor, existing + score);\n\n            const prev = provenance.get(neighbor);\n            if (\n              !prev ||\n              hop + 1 < prev.hopDepth ||\n              (hop + 1 === prev.hopDepth && score > prev.decayedWeight)\n            ) {\n              provenance.set(neighbor, {\n                seed: sourceSeed,\n                hopDepth: hop + 1,\n                decayedWeight: score,\n                graphType: edge.type,\n                edgeConfidence: conf,\n              });\n            }\n          }\n\n          if (!visited.has(neighbor)) {\n            visited.add(neighbor);\n            queue.push([neighbor, hop + 1, sourceSeed]);\n          }\n        }\n      }\n\n      // Issue #681 PR 3/3 — optional PageRank-style refinement.\n      // Redistributes a node's accumulated activation along its outgoing\n      // edges, weighted by edge confidence. Damping is fixed at the\n      // canonical 0.85 so the ranking stays comparable across queries;\n      // the `iterations` knob bounds compute, not behavior shape.\n      if (iterations > 0 && scores.size > 1) {\n        applyPageRankRefinement(scores, adj, {\n          iterations,\n          floor,\n          damping: 0.85,\n        });\n      }\n\n      // Apply lateral inhibition if enabled (Synapse-inspired competitive suppression)\n      if (this.cfg.graphLateralInhibitionEnabled && scores.size > 1) {\n        const inhibited = applyLateralInhibition(scores, {\n          beta: this.cfg.graphLateralInhibitionBeta,\n          topM: this.cfg.graphLateralInhibitionTopM,\n        });\n        for (const [k, v] of inhibited) {\n          scores.set(k, v);\n        }\n      }\n\n      return Array.from(scores.entries())\n        .map(([p, score]) => ({\n          path: p,\n          score,\n          seed: provenance.get(p)?.seed ?? \"\",\n          hopDepth: provenance.get(p)?.hopDepth ?? 0,\n          decayedWeight: provenance.get(p)?.decayedWeight ?? 0,\n          graphType: provenance.get(p)?.graphType ?? \"entity\",\n          edgeConfidence: provenance.get(p)?.edgeConfidence ?? 1,\n        }))\n        .sort((a, b) => b.score - a.score);\n    } catch (err) {\n      const { log } = await import(\"./logger.js\");\n      log.warn(`[graph] spreadingActivation error: ${err}`);\n      return [];\n    }\n  }\n}\n\n/**\n * Clamp `graphTraversalConfidenceFloor` into the legal range `[0, 1]`.\n * Non-finite or non-numeric values fall back to the documented default\n * so misconfiguration cannot silently disable the floor or reject every edge.\n *\n * Exported for tests; call sites in `spreadingActivation` use it to make\n * the contract explicit at every boundary.\n */\nexport function clampConfidenceFloor(raw: unknown): number {\n  if (typeof raw !== \"number\" || !Number.isFinite(raw)) {\n    return DEFAULT_GRAPH_TRAVERSAL_CONFIDENCE_FLOOR;\n  }\n  if (raw < 0) return 0;\n  if (raw > 1) return 1;\n  return raw;\n}\n\n/**\n * Clamp `graphTraversalPageRankIterations` into a non-negative integer.\n * Negative or non-finite values fall back to 0 (disable refinement) so\n * misconfiguration cannot stall recall in an unbounded loop.\n */\nexport function clampPageRankIterations(raw: unknown): number {\n  if (typeof raw !== \"number\" || !Number.isFinite(raw)) return 0;\n  if (raw <= 0) return 0;\n  return Math.floor(raw);\n}\n\n/**\n * PageRank-style refinement on top of the BFS activation map.\n *\n * Each iteration redistributes a fraction of every node's score along\n * its outgoing edges, scaled by edge confidence. Confidence below\n * `floor` is filtered out before redistribution, mirroring the BFS\n * pruning rule. Mutates `scores` in place.\n *\n * Exported for tests; in production, call sites pass the same adjacency\n * map already used by BFS so behavior stays consistent.\n */\nexport function applyPageRankRefinement(\n  scores: Map<string, number>,\n  adj: Map<string, GraphEdge[]>,\n  opts: { iterations: number; floor: number; damping: number },\n): void {\n  const { iterations, floor, damping } = opts;\n  if (iterations <= 0 || scores.size === 0) return;\n  const safeDamping = Math.min(1, Math.max(0, damping));\n\n  // Pre-compute confidence-weighted out-edge totals for normalization.\n  // Done once per refinement, not per iteration, since adjacency is\n  // immutable inside the loop.\n  //\n  // Codex P1 (#735): the denominator MUST be computed over the same\n  // eligible-neighbor set the iteration redistributes into — i.e.\n  // edges whose neighbor is in `scores`. Counting edges-to-seeds (or\n  // edges-to-unseen-nodes) in the denominator while dropping their\n  // flow during iteration leaks `safeDamping × score` every pass and\n  // collapses leaf candidates' scores instead of just re-ranking them.\n  const eligible = (edge: GraphEdge, fromNode: string): boolean => {\n    if (readEdgeConfidence(edge) < floor) return false;\n    const neighbor = edge.to === fromNode ? edge.from : edge.to;\n    return scores.has(neighbor);\n  };\n  const outboundTotal = new Map<string, number>();\n  for (const [node, edges] of adj.entries()) {\n    if (!scores.has(node)) continue; // only candidate nodes redistribute\n    let sum = 0;\n    for (const edge of edges) {\n      if (!eligible(edge, node)) continue;\n      sum += readEdgeConfidence(edge) * edge.weight;\n    }\n    if (sum > 0) outboundTotal.set(node, sum);\n  }\n\n  for (let i = 0; i < iterations; i += 1) {\n    const next = new Map<string, number>();\n    // Teleport / damping floor: every node retains `(1 - damping) * score`\n    // of its current activation so dangling nodes do not bleed to zero.\n    for (const [node, score] of scores) {\n      next.set(node, (1 - safeDamping) * score);\n    }\n    for (const [node, score] of scores) {\n      const outEdges = adj.get(node);\n      const total = outboundTotal.get(node);\n      // Dangling-node fallback: when a candidate has zero eligible\n      // outflow (no in-scores neighbors above the floor), the\n      // `safeDamping × score` portion would otherwise evaporate. Keep\n      // it on `node` so total mass is conserved and the score reflects\n      // the candidate's standing rather than its in-degree topology.\n      if (!outEdges || outEdges.length === 0 || !total || total <= 0) {\n        next.set(node, (next.get(node) ?? 0) + safeDamping * score);\n        continue;\n      }\n      for (const edge of outEdges) {\n        if (!eligible(edge, node)) continue;\n        const conf = readEdgeConfidence(edge);\n        const neighbor = edge.to === node ? edge.from : edge.to;\n        const flow = safeDamping * score * ((conf * edge.weight) / total);\n        next.set(neighbor, (next.get(neighbor) ?? 0) + flow);\n      }\n    }\n    for (const [node, score] of next) {\n      scores.set(node, score);\n    }\n  }\n}\n\n/**\n * Lateral inhibition (Synapse-inspired).\n *\n * For each node, the top-M higher-activation competitors exert inhibition\n * proportional to their activation difference. Output is clamped to [0, ∞).\n *\n * No sigmoid is applied here — downstream `normalizeGraphActivationScore`\n * already applies x/(1+x) soft squash, so adding a sigmoid would double-\n * normalize and cap graph influence at ~50%.\n *\n * Formula: u_hat_i = max(0, u_i - beta * sum_{k in top-M where u_k > u_i}(u_k - u_i))\n *\n * When beta=0 or topM=0, returns original scores unchanged (no-op).\n */\nexport function applyLateralInhibition(\n  scores: Map<string, number>,\n  opts: { beta: number; topM: number },\n): Map<string, number> {\n  const { beta, topM } = opts;\n  if (beta === 0 || topM === 0) return new Map(scores);\n\n  const sorted = Array.from(scores.entries()).sort((a, b) => b[1] - a[1]);\n  const topCompetitors = sorted.slice(0, topM);\n\n  const result = new Map<string, number>();\n  for (const [node, u] of scores) {\n    let inhibition = 0;\n    for (const [, uK] of topCompetitors) {\n      if (uK > u) {\n        inhibition += uK - u;\n      }\n    }\n    result.set(node, Math.max(0, u - beta * inhibition));\n  }\n\n  return 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