fix(#92): finalize semantic neighbor naming — remove remaining Metroid references from neighbor graph code

Closes #92

Co-authored-by: devlux76 <[email protected]>

Author: Copilot

lib/daydreamer/ClusterStability.ts

@@ -52,7 +52,7 @@ export interface LabelPropagationResult {
 /**
  * Run one pass of label propagation over all pages.
  *
- * Each node adopts the most frequent label among its Metroid neighbors.
+ * Each node adopts the most frequent label among its semantic neighbors.
  * Ties are broken deterministically by choosing the lexicographically
  * smallest label (consistent across runs and nodes).
  *
@@ -107,7 +107,7 @@ async function propagationPass(
 
 /**
  * Assign community labels to all pages via label propagation on the
- * Metroid (semantic) neighbor graph.
+ * Semantic neighbor graph.
  *
  * Initial labels: each page is its own community (pageId as initial label).
  * Each iteration: every node adopts the most frequent label among neighbors.

lib/daydreamer/FullNeighborRecalc.ts

@@ -31,7 +31,7 @@ export interface FullNeighborRecalcOptions {
   metadataStore: MetadataStore;
   vectorStore: VectorStore;
   policy?: HotpathPolicy;
-  /** Maximum Metroid neighbors stored per page. Default: 16. */
+  /** Maximum semantic neighbors stored per page. Default: 16. */
   maxNeighbors?: number;
   /** Current timestamp (ms since epoch). Defaults to Date.now(). */
   now?: number;
@@ -71,7 +71,7 @@ function cosineSimilarity(a: Float32Array, b: Float32Array): number {
  *
  * Finds all volumes flagged as dirty (via `needsNeighborRecalc`), loads
  * their pages, computes pairwise cosine similarities, and updates the
- * Metroid neighbor index. Processing is bounded by the Williams-Bound-derived
+ * semantic neighbor index. Processing is bounded by the Williams-Bound-derived
  * maintenance budget to avoid blocking the idle loop.
  *
  * After recalculation, salience is recomputed for affected pages and a

lib/sharing/SubgraphExporter.ts

@@ -83,9 +83,9 @@ async function expandSeeds(
     for (const pageId of frontier) {
       if (collectedPages.length >= maxNodes) break;
 
-      // Expand via Metroid (semantic) neighbors
-      const metroidNeighbors: SemanticNeighbor[] = await metadataStore.getSemanticNeighbors(pageId);
-      for (const n of metroidNeighbors) {
+      // Expand via semantic neighbors
+      const semanticNeighbors: SemanticNeighbor[] = await metadataStore.getSemanticNeighbors(pageId);
+      for (const n of semanticNeighbors) {
         if (!visited.has(n.neighborPageId) && collectedPages.length < maxNodes) {
           visited.add(n.neighborPageId);
           nextFrontier.push(n.neighborPageId);

lib/storage/IndexedDbMetadataStore.ts

@@ -96,7 +96,7 @@ function applyUpgrade(db: IDBDatabase): void {
     db.createObjectStore(STORE.pageActivity, { keyPath: "pageId" });
   }
 
-  // v3 stores — neighbor_graph (replaces the old metroid_neighbors name)
+  // v3 stores — neighbor_graph (semantic neighbor proximity index)
   if (!db.objectStoreNames.contains(STORE.neighborGraph)) {
     db.createObjectStore(STORE.neighborGraph, { keyPath: "pageId" });
   }

tests/SalienceEngine.test.ts

@@ -118,12 +118,7 @@ class MockMetadataStore implements MetadataStore {
   async getBooksByPage(): Promise<never[]> { return []; }
   async getVolumesByBook(): Promise<never[]> { return []; }
   async getShelvesByVolume(): Promise<never[]> { return []; }
-  async putMetroidNeighbors(): Promise<void> { /* stub */ }
-  async getMetroidNeighbors(): Promise<never[]> { return []; }
-  async getInducedMetroidSubgraph() { return { nodes: [], edges: [] }; }
-  async needsMetroidRecalc(): Promise<boolean> { return false; }
-  async flagVolumeForMetroidRecalc(): Promise<void> { /* stub */ }
-  async clearMetroidRecalcFlag(): Promise<void> { /* stub */ }
+
   async deleteEdge(): Promise<void> { /* stub */ }
   async putSemanticNeighbors(): Promise<void> { /* stub */ }
   async getSemanticNeighbors(): Promise<never[]> { return []; }

tests/daydreamer/ClusterStability.test.ts

@@ -350,7 +350,7 @@ class MockMetadataStore implements MetadataStore {
     return [...this.shelves.values()].filter((s) => s.volumeIds.includes(volumeId));
   }
 
-  // Metroid / Semantic neighbor stubs
+  // Semantic neighbor stubs
   async putSemanticNeighbors(): Promise<void> { /* stub */ }
   async getSemanticNeighbors(): Promise<SemanticNeighbor[]> { return []; }
   async getInducedNeighborSubgraph(): Promise<SemanticNeighborSubgraph> { return { nodes: [], edges: [] }; }

tests/daydreamer/FullNeighborRecalc.test.ts

@@ -71,7 +71,7 @@ class FullMockMetadataStore implements MetadataStore {
   private edgeMap = new Map<string, Edge>();
   private activities = new Map<Hash, PageActivity>();
   private hotpath = new Map<Hash, HotpathEntry>();
-  private metroidNeighbors = new Map<Hash, SemanticNeighbor[]>();
+  private semanticNeighbors = new Map<Hash, SemanticNeighbor[]>();
   private dirtyFlags = new Map<Hash, boolean>();
 
   async putPage(page: Page) { this.pages.set(page.pageId, page); }
@@ -103,10 +103,10 @@ class FullMockMetadataStore implements MetadataStore {
   async getShelvesByVolume() { return []; }
 
   async putSemanticNeighbors(pageId: Hash, neighbors: SemanticNeighbor[]) {
-    this.metroidNeighbors.set(pageId, [...neighbors]);
+    this.semanticNeighbors.set(pageId, [...neighbors]);
   }
   async getSemanticNeighbors(pageId: Hash) {
-    return this.metroidNeighbors.get(pageId) ?? [];
+    return this.semanticNeighbors.get(pageId) ?? [];
   }
   async getInducedNeighborSubgraph(): Promise<SemanticNeighborSubgraph> { return { nodes: [], edges: [] }; }
 
@@ -132,7 +132,7 @@ class FullMockMetadataStore implements MetadataStore {
   async getPageActivity(id: Hash) { return this.activities.get(id); }
 
   isDirty(volumeId: Hash): boolean { return this.dirtyFlags.get(volumeId) === true; }
-  getSemanticNeighborsSync(pageId: Hash) { return this.metroidNeighbors.get(pageId) ?? []; }
+  getSemanticNeighborsSync(pageId: Hash) { return this.semanticNeighbors.get(pageId) ?? []; }
 }
 
 // ---------------------------------------------------------------------------

tests/daydreamer/HebbianUpdater.test.ts

@@ -58,7 +58,7 @@ class FullMockMetadataStore implements MetadataStore {
   private edgeMap = new Map<string, Edge>();
   private activities = new Map<Hash, PageActivity>();
   private hotpath = new Map<Hash, HotpathEntry>();
-  private metroidNeighbors = new Map<Hash, SemanticNeighbor[]>();
+  private semanticNeighbors = new Map<Hash, SemanticNeighbor[]>();
   private dirtyFlags = new Map<Hash, boolean>();
 
   async putPage(page: Page) { this.pages.set(page.pageId, page); }
@@ -94,10 +94,10 @@ class FullMockMetadataStore implements MetadataStore {
   async getShelvesByVolume() { return []; }
 
   async putSemanticNeighbors(pageId: Hash, neighbors: SemanticNeighbor[]) {
-    this.metroidNeighbors.set(pageId, neighbors);
+    this.semanticNeighbors.set(pageId, neighbors);
   }
   async getSemanticNeighbors(pageId: Hash) {
-    return this.metroidNeighbors.get(pageId) ?? [];
+    return this.semanticNeighbors.get(pageId) ?? [];
   }
   async getInducedNeighborSubgraph(): Promise<SemanticNeighborSubgraph> { return { nodes: [], edges: [] }; }
 

tests/daydreamer/PrototypeRecomputer.test.ts

@@ -72,7 +72,7 @@ class FullMockMetadataStore implements MetadataStore {
   private edgeMap = new Map<string, Edge>();
   private activities = new Map<Hash, PageActivity>();
   private hotpath = new Map<Hash, HotpathEntry>();
-  private metroidNeighbors = new Map<Hash, SemanticNeighbor[]>();
+  private semanticNeighbors = new Map<Hash, SemanticNeighbor[]>();
   private dirtyFlags = new Map<Hash, boolean>();
 
   async putPage(page: Page) { this.pages.set(page.pageId, page); }
@@ -111,9 +111,9 @@ class FullMockMetadataStore implements MetadataStore {
   async getShelvesByVolume() { return []; }
 
   async putSemanticNeighbors(pageId: Hash, neighbors: SemanticNeighbor[]) {
-    this.metroidNeighbors.set(pageId, neighbors);
+    this.semanticNeighbors.set(pageId, neighbors);
   }
-  async getSemanticNeighbors(pageId: Hash) { return this.metroidNeighbors.get(pageId) ?? []; }
+  async getSemanticNeighbors(pageId: Hash) { return this.semanticNeighbors.get(pageId) ?? []; }
   async getInducedNeighborSubgraph(): Promise<SemanticNeighborSubgraph> { return { nodes: [], edges: [] }; }
 
   async needsNeighborRecalc(id: Hash) { return this.dirtyFlags.get(id) === true; }

tests/sharing/SubgraphExchange.test.ts

@@ -66,7 +66,7 @@ class FullMockMetadataStore implements MetadataStore {
   private edgeMap = new Map<string, Edge>();
   private activities = new Map<Hash, PageActivity>();
   private hotpath = new Map<Hash, HotpathEntry>();
-  private metroidNeighbors = new Map<Hash, SemanticNeighbor[]>();
+  private semanticNeighbors = new Map<Hash, SemanticNeighbor[]>();
   private dirtyFlags = new Map<Hash, boolean>();
 
   async putPage(page: Page) { this.pages.set(page.pageId, page); }
@@ -96,9 +96,9 @@ class FullMockMetadataStore implements MetadataStore {
   async getShelvesByVolume() { return []; }
 
   async putSemanticNeighbors(pageId: Hash, neighbors: SemanticNeighbor[]) {
-    this.metroidNeighbors.set(pageId, neighbors);
+    this.semanticNeighbors.set(pageId, neighbors);
   }
-  async getSemanticNeighbors(pageId: Hash) { return this.metroidNeighbors.get(pageId) ?? []; }
+  async getSemanticNeighbors(pageId: Hash) { return this.semanticNeighbors.get(pageId) ?? []; }
   async getInducedNeighborSubgraph(): Promise<SemanticNeighborSubgraph> { return { nodes: [], edges: [] }; }
 
   async needsNeighborRecalc(id: Hash) { return this.dirtyFlags.get(id) === true; }