@velvetmonkey/flywheel-memory 2.0.156 → 2.0.157

package/dist/index.js

@@ -575,7 +575,7 @@ function getStoredEmbeddingModel() {
 function diagnoseEmbeddings(vaultPath2) {
   const db4 = getDb();
   const checks = [];
-  const counts = { embedded: 0, vaultNotes: 0, orphaned: 0, missing: 0 };
+  const counts = { embedded: 0, vaultNotes: 0, orphaned: 0, orphanedEntities: 0, missing: 0 };
   if (!db4) {
     checks.push({ name: "database", status: "stale", detail: "No database available" });
     return { healthy: false, checks, counts };
@@ -649,6 +649,25 @@ function diagnoseEmbeddings(vaultPath2) {
   } catch {
     checks.push({ name: "orphans", status: "warning", detail: "Could not check" });
   }
+  try {
+    const embNames = new Set(
+      db4.prepare("SELECT entity_name FROM entity_embeddings").all().map((r) => r.entity_name)
+    );
+    const entityNames = new Set(
+      db4.prepare("SELECT name FROM entities").all().map((r) => r.name)
+    );
+    counts.orphanedEntities = 0;
+    for (const n of embNames) {
+      if (!entityNames.has(n)) counts.orphanedEntities++;
+    }
+    if (counts.orphanedEntities > 0) {
+      checks.push({ name: "entity_orphans", status: "warning", detail: `${counts.orphanedEntities} orphaned entity embeddings` });
+    } else {
+      checks.push({ name: "entity_orphans", status: "ok", detail: "0 orphaned" });
+    }
+  } catch {
+    checks.push({ name: "entity_orphans", status: "ok", detail: "No entity embeddings table" });
+  }
   try {
     const samples = db4.prepare("SELECT embedding FROM note_embeddings ORDER BY RANDOM() LIMIT 3").all();
     let corrupt = false;
@@ -732,6 +751,7 @@ async function buildEntityEmbeddingsIndex(vaultPath2, entities, onProgress) {
   const total = entities.size;
   let done = 0;
   let updated = 0;
+  let skipped = 0;
   for (const [name, entity] of entities) {
     done++;
     try {
@@ -745,7 +765,11 @@ async function buildEntityEmbeddingsIndex(vaultPath2, entities, onProgress) {
       const buf = Buffer.from(embedding.buffer, embedding.byteOffset, embedding.byteLength);
       upsert.run(name, buf, hash, activeModelConfig.id, Date.now());
       updated++;
-    } catch {
+    } catch (err) {
+      skipped++;
+      if (skipped <= 3) {
+        console.error(`[Semantic] Failed to embed entity ${name}: ${err instanceof Error ? err.message : err}`);
+      }
     }
     if (onProgress) onProgress(done, total);
   }
@@ -755,7 +779,7 @@ async function buildEntityEmbeddingsIndex(vaultPath2, entities, onProgress) {
       deleteStmt.run(existingName);
     }
   }
-  console.error(`[Semantic] Entity embeddings: ${updated} updated, ${total - updated} unchanged`);
+  console.error(`[Semantic] Entity embeddings: ${updated} updated, ${total - updated - skipped} unchanged, ${skipped} failed`);
   return updated;
 }
 async function updateEntityEmbedding(entityName, entity, vaultPath2) {
@@ -773,9 +797,34 @@ async function updateEntityEmbedding(entityName, entity, vaultPath2) {
       VALUES (?, ?, ?, ?, ?)
     `).run(entityName, buf, hash, activeModelConfig.id, Date.now());
     entityEmbeddingsMap.set(entityName, embedding);
-  } catch {
+  } catch (err) {
+    console.error(`[Semantic] Failed to update entity embedding ${entityName}: ${err instanceof Error ? err.message : err}`);
   }
 }
+function removeOrphanedNoteEmbeddings() {
+  const db4 = getDb();
+  if (!db4) return 0;
+  const result = db4.prepare(
+    "DELETE FROM note_embeddings WHERE path NOT IN (SELECT path FROM notes_fts)"
+  ).run();
+  return result.changes;
+}
+function removeOrphanedEntityEmbeddings(currentEntityNames) {
+  const db4 = getDb();
+  if (!db4) return 0;
+  const rows = db4.prepare("SELECT entity_name FROM entity_embeddings").all();
+  const deleteStmt = db4.prepare("DELETE FROM entity_embeddings WHERE entity_name = ?");
+  const embMap = getEmbMap();
+  let removed = 0;
+  for (const row of rows) {
+    if (!currentEntityNames.has(row.entity_name)) {
+      deleteStmt.run(row.entity_name);
+      embMap.delete(row.entity_name);
+      removed++;
+    }
+  }
+  return removed;
+}
 function findSemanticallySimilarEntities(queryEmbedding, limit, excludeEntities) {
   const scored = [];
   for (const [entityName, embedding] of getEmbMap()) {
@@ -8703,8 +8752,9 @@ var PipelineRunner = class {
         } catch {
         }
       }
-      tracker.end({ updated: embUpdated, removed: embRemoved });
-      serverLog("watcher", `Note embeddings: ${embUpdated} updated, ${embRemoved} removed`);
+      const orphansRemoved = removeOrphanedNoteEmbeddings();
+      tracker.end({ updated: embUpdated, removed: embRemoved, orphans_removed: orphansRemoved });
+      serverLog("watcher", `Note embeddings: ${embUpdated} updated, ${embRemoved} removed, ${orphansRemoved} orphans cleaned`);
     } else {
       tracker.skip("note_embeddings", "not built");
     }
@@ -8715,6 +8765,7 @@ var PipelineRunner = class {
     if (hasEntityEmbeddingsIndex() && p.sd) {
       tracker.start("entity_embeddings", { files: p.events.length });
       let entEmbUpdated = 0;
+      let entEmbOrphansRemoved = 0;
       const entEmbNames = [];
       try {
         const allEntities = getAllEntitiesFromDb(p.sd);
@@ -8732,10 +8783,12 @@ var PipelineRunner = class {
             entEmbNames.push(entity.name);
           }
         }
+        const currentNames = new Set(allEntities.map((e) => e.name));
+        entEmbOrphansRemoved = removeOrphanedEntityEmbeddings(currentNames);
       } catch {
       }
-      tracker.end({ updated: entEmbUpdated, updated_entities: entEmbNames.slice(0, 10) });
-      serverLog("watcher", `Entity embeddings: ${entEmbUpdated} updated`);
+      tracker.end({ updated: entEmbUpdated, updated_entities: entEmbNames.slice(0, 10), orphans_removed: entEmbOrphansRemoved });
+      serverLog("watcher", `Entity embeddings: ${entEmbUpdated} updated, ${entEmbOrphansRemoved} orphans cleaned`);
     } else {
       tracker.skip("entity_embeddings", !p.sd ? "no sd" : "not built");
     }
@@ -9283,9 +9336,10 @@ var PipelineRunner = class {
       return { skipped: true, reason: "vacuumed recently" };
     }
     p.sd.db.pragma("incremental_vacuum");
+    p.sd.db.pragma("wal_checkpoint(TRUNCATE)");
     p.sd.setMetadataValue.run("last_incremental_vacuum", String(Date.now()));
-    serverLog("watcher", "Incremental vacuum completed");
-    return { vacuumed: true };
+    serverLog("watcher", "Incremental vacuum + WAL checkpoint completed");
+    return { vacuumed: true, wal_checkpointed: true };
   }
 };
 
@@ -24932,7 +24986,8 @@ function registerAllTools(targetServer, ctx) {
 var __filename = fileURLToPath2(import.meta.url);
 var __dirname = dirname7(__filename);
 var pkg = JSON.parse(readFileSync6(join21(__dirname, "../package.json"), "utf-8"));
-var vaultPath = process.env.PROJECT_PATH || process.env.VAULT_PATH || findVaultRoot();
+var _earlyVaultConfigs = parseVaultConfig();
+var vaultPath = _earlyVaultConfigs ? _earlyVaultConfigs[0].path : process.env.PROJECT_PATH || process.env.VAULT_PATH || findVaultRoot();
 var resolvedVaultPath;
 try {
   resolvedVaultPath = realpathSync(vaultPath).replace(/\\/g, "/");
@@ -25210,7 +25265,7 @@ async function main() {
   serverLog("server", `Starting Flywheel Memory v${pkg.version}...`);
   serverLog("server", `Vault: ${vaultPath}`);
   const startTime = Date.now();
-  const vaultConfigs = parseVaultConfig();
+  const vaultConfigs = _earlyVaultConfigs;
   if (vaultConfigs) {
     vaultRegistry = new VaultRegistry(vaultConfigs[0].name);
     serverLog("server", `Multi-vault mode: ${vaultConfigs.map((v) => v.name).join(", ")}`);

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@velvetmonkey/flywheel-memory",
-  "version": "2.0.156",
+  "version": "2.0.157",
   "description": "MCP tools that search, write, and auto-link your Obsidian vault — and learn from your edits.",
   "type": "module",
   "main": "dist/index.js",
@@ -54,7 +54,7 @@
   "dependencies": {
     "@huggingface/transformers": "^3.8.1",
     "@modelcontextprotocol/sdk": "^1.25.1",
-    "@velvetmonkey/vault-core": "^2.0.156",
+    "@velvetmonkey/vault-core": "^2.0.157",
     "better-sqlite3": "^12.0.0",
     "chokidar": "^4.0.0",
     "gray-matter": "^4.0.3",