@199-bio/engram 0.8.0 → 0.8.1

package/dist/consolidation/consolidator.d.ts.map

@@ -1 +1 @@
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package/dist/index.js

@@ -10,6 +10,7 @@ import { StdioServerTransport } from "@modelcontextprotocol/sdk/server/stdio.js"
 import { CallToolRequestSchema, ListToolsRequestSchema, } from "@modelcontextprotocol/sdk/types.js";
 import path from "path";
 import os from "os";
+import fs from "fs";
 import { EngramDatabase } from "./storage/database.js";
 import { KnowledgeGraph } from "./graph/knowledge-graph.js";
 import { createRetriever } from "./retrieval/colbert.js";
@@ -21,6 +22,94 @@ const DB_PATH = process.env.ENGRAM_DB_PATH
     ? path.resolve(process.env.ENGRAM_DB_PATH.replace("~", os.homedir()))
     : path.join(os.homedir(), ".engram");
 const DB_FILE = path.join(DB_PATH, "engram.db");
+const PID_FILE = path.join(DB_PATH, "engram.pid");
+// ============ Zombie Prevention ============
+/**
+ * Kill any existing engram process and clean up stale PID file
+ */
+function cleanupZombies() {
+    try {
+        if (fs.existsSync(PID_FILE)) {
+            const oldPid = parseInt(fs.readFileSync(PID_FILE, "utf-8").trim(), 10);
+            if (oldPid && oldPid !== process.pid) {
+                try {
+                    // Check if process exists
+                    process.kill(oldPid, 0);
+                    // It exists, kill it
+                    console.error(`[Engram] Killing old instance (PID ${oldPid})`);
+                    process.kill(oldPid, "SIGTERM");
+                }
+                catch {
+                    // Process doesn't exist, that's fine
+                }
+            }
+            fs.unlinkSync(PID_FILE);
+        }
+    }
+    catch (error) {
+        console.error("[Engram] Error cleaning up zombies:", error);
+    }
+}
+/**
+ * Write our PID file
+ */
+function writePidFile() {
+    try {
+        // Ensure directory exists
+        if (!fs.existsSync(DB_PATH)) {
+            fs.mkdirSync(DB_PATH, { recursive: true });
+        }
+        fs.writeFileSync(PID_FILE, String(process.pid));
+    }
+    catch (error) {
+        console.error("[Engram] Error writing PID file:", error);
+    }
+}
+/**
+ * Clean up on exit
+ */
+function cleanup() {
+    try {
+        if (fs.existsSync(PID_FILE)) {
+            const storedPid = parseInt(fs.readFileSync(PID_FILE, "utf-8").trim(), 10);
+            if (storedPid === process.pid) {
+                fs.unlinkSync(PID_FILE);
+            }
+        }
+        if (webServer) {
+            webServer.stop();
+        }
+        if (db) {
+            db.close();
+        }
+    }
+    catch {
+        // Ignore cleanup errors
+    }
+}
+// Register signal handlers early
+process.on("SIGTERM", () => {
+    console.error("[Engram] Received SIGTERM, shutting down...");
+    cleanup();
+    process.exit(0);
+});
+process.on("SIGINT", () => {
+    console.error("[Engram] Received SIGINT, shutting down...");
+    cleanup();
+    process.exit(0);
+});
+process.on("exit", cleanup);
+// Detect when parent process (Claude) dies by monitoring stdin
+process.stdin.on("end", () => {
+    console.error("[Engram] stdin closed, parent process likely died. Shutting down...");
+    cleanup();
+    process.exit(0);
+});
+process.stdin.on("close", () => {
+    console.error("[Engram] stdin closed, shutting down...");
+    cleanup();
+    process.exit(0);
+});
 // ============ Initialize Components ============
 let db;
 let graph;
@@ -540,9 +629,9 @@ server.setRequestHandler(CallToolRequestSchema, async (request) => {
             }
             case "memory_feedback": {
                 const { recall_id, useful_memory_ids, need_more = false } = args;
-                // Update the retrieval log with feedback
-                const updated = db.updateRetrievalFeedback(recall_id, useful_memory_ids, need_more);
-                if (!updated) {
+                // First, get the original recall to validate useful_memory_ids
+                const retrievalLog = db.getRetrievalLog(recall_id);
+                if (!retrievalLog) {
                     return {
                         content: [
                             {
@@ -555,6 +644,30 @@ server.setRequestHandler(CallToolRequestSchema, async (request) => {
                         ],
                     };
                 }
+                // Validate: only accept IDs that were in the original recall
+                const originalIdSet = new Set(retrievalLog.memory_ids);
+                const validUsefulIds = useful_memory_ids.filter(id => originalIdSet.has(id));
+                const invalidIds = useful_memory_ids.filter(id => !originalIdSet.has(id));
+                if (invalidIds.length > 0) {
+                    console.error(`[Engram] memory_feedback: ${invalidIds.length} IDs not in original recall, ignored: ${invalidIds.join(", ")}`);
+                }
+                // Update the retrieval log with validated feedback
+                const updated = db.updateRetrievalFeedback(recall_id, validUsefulIds, need_more);
+                if (!updated) {
+                    // Should not happen since we already checked above, but handle gracefully
+                    console.error(`[Engram] memory_feedback: failed to update retrieval log ${recall_id}`);
+                    return {
+                        content: [
+                            {
+                                type: "text",
+                                text: JSON.stringify({
+                                    success: false,
+                                    error: `Failed to update feedback for: ${recall_id}`,
+                                }),
+                            },
+                        ],
+                    };
+                }
                 // If need_more is set, do an expanded search
                 if (need_more) {
                     const expandedResponse = await search.expandSearch(recall_id);
@@ -576,7 +689,7 @@ server.setRequestHandler(CallToolRequestSchema, async (request) => {
                                 text: JSON.stringify({
                                     success: true,
                                     feedback_recorded: true,
-                                    useful_count: useful_memory_ids.length,
+                                    useful_count: validUsefulIds.length,
                                     expanded_search: true,
                                     additional_results: formatted,
                                     additional_count: formatted.length,
@@ -605,7 +718,7 @@ server.setRequestHandler(CallToolRequestSchema, async (request) => {
                             text: JSON.stringify({
                                 success: true,
                                 feedback_recorded: true,
-                                useful_count: useful_memory_ids.length,
+                                useful_count: validUsefulIds.length,
                                 learning_applied: learningApplied > 0,
                                 connections_strengthened: learningApplied,
                             }, null, 2),
@@ -632,10 +745,13 @@ server.setRequestHandler(CallToolRequestSchema, async (request) => {
 });
 // ============ Main ============
 async function main() {
+    // Kill any zombie instances before starting
+    cleanupZombies();
+    writePidFile();
     await initialize();
     const transport = new StdioServerTransport();
     await server.connect(transport);
-    console.error("[Engram] MCP server running on stdio");
+    console.error(`[Engram] MCP server running on stdio (PID ${process.pid})`);
 }
 main().catch((error) => {
     console.error("[Engram] Fatal error:", error);

package/dist/retrieval/hybrid.d.ts.map

@@ -1 +1 @@
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package/dist/storage/database.d.ts.map

@@ -1 +1 @@
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package/dist/web/chat-handler.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"chat-handler.d.ts","sourceRoot":"","sources":["../../src/web/chat-handler.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAGH,OAAO,EAAE,cAAc,EAAkB,MAAM,wBAAwB,CAAC;AACxE,OAAO,EAAE,cAAc,EAAE,MAAM,6BAA6B,CAAC;AAC7D,OAAO,EAAE,YAAY,EAAE,MAAM,wBAAwB,CAAC;AAoQtD,MAAM,WAAW,WAAW;IAC1B,IAAI,EAAE,MAAM,GAAG,YAAY,GAAG,UAAU,GAAG,OAAO,GAAG,MAAM,CAAC;IAC5D,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,MAAM,CAAC,EAAE,OAAO,CAAC;CAClB;AAED,qBAAa,WAAW;IACtB,OAAO,CAAC,MAAM,CAA0B;IACxC,OAAO,CAAC,EAAE,CAAiB;IAC3B,OAAO,CAAC,KAAK,CAAiB;IAC9B,OAAO,CAAC,MAAM,CAAe;IAC7B,OAAO,CAAC,mBAAmB,CAAgC;IAC3D,OAAO,CAAC,YAAY,CAAkB;IACtC,OAAO,CAAC,YAAY,CAAoG;gBAE5G,OAAO,EAAE;QACnB,EAAE,EAAE,cAAc,CAAC;QACnB,KAAK,EAAE,cAAc,CAAC;QACtB,MAAM,EAAE,YAAY,CAAC;KACtB;IASD;;OAEG;IACH,aAAa,IAAI,IAAI;IASrB,YAAY,IAAI,OAAO;IAIvB,MAAM,IAAI,OAAO;IAIjB,cAAc,IAAI,MAAM;IAIxB,YAAY,IAAI,IAAI;YAKN,YAAY;IAgBpB,IAAI,CAAC,WAAW,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,CAAC;IAgBzC,UAAU,CAAC,WAAW,EAAE,MAAM,GAAG,cAAc,CAAC,WAAW,CAAC;YAsHrD,cAAc;YAgFd,WAAW;CAoQ1B"}
+{"version":3,"file":"chat-handler.d.ts","sourceRoot":"","sources":["../../src/web/chat-handler.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAGH,OAAO,EAAE,cAAc,EAAkB,MAAM,wBAAwB,CAAC;AACxE,OAAO,EAAE,cAAc,EAAE,MAAM,6BAA6B,CAAC;AAC7D,OAAO,EAAE,YAAY,EAAE,MAAM,wBAAwB,CAAC;AAwQtD,MAAM,WAAW,WAAW;IAC1B,IAAI,EAAE,MAAM,GAAG,YAAY,GAAG,UAAU,GAAG,OAAO,GAAG,MAAM,CAAC;IAC5D,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,MAAM,CAAC,EAAE,OAAO,CAAC;CAClB;AAED,qBAAa,WAAW;IACtB,OAAO,CAAC,MAAM,CAA0B;IACxC,OAAO,CAAC,EAAE,CAAiB;IAC3B,OAAO,CAAC,KAAK,CAAiB;IAC9B,OAAO,CAAC,MAAM,CAAe;IAC7B,OAAO,CAAC,mBAAmB,CAAgC;IAC3D,OAAO,CAAC,YAAY,CAAkB;IACtC,OAAO,CAAC,YAAY,CAAoG;gBAE5G,OAAO,EAAE;QACnB,EAAE,EAAE,cAAc,CAAC;QACnB,KAAK,EAAE,cAAc,CAAC;QACtB,MAAM,EAAE,YAAY,CAAC;KACtB;IASD;;OAEG;IACH,aAAa,IAAI,IAAI;IAYrB,YAAY,IAAI,OAAO;IAMvB,MAAM,IAAI,OAAO;IAIjB,cAAc,IAAI,MAAM;IAIxB,YAAY,IAAI,IAAI;YAKN,YAAY;IAgBpB,IAAI,CAAC,WAAW,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,CAAC;IAiBzC,UAAU,CAAC,WAAW,EAAE,MAAM,GAAG,cAAc,CAAC,WAAW,CAAC;YA6GrD,cAAc;YAkFd,WAAW;CAoQ1B"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@199-bio/engram",
-  "version": "0.8.0",
+  "version": "0.8.1",
   "description": "Give Claude a perfect memory. Local-first MCP server with hybrid search.",
   "type": "module",
   "main": "dist/index.js",

package/src/consolidation/consolidator.ts

@@ -112,6 +112,7 @@ interface ConsolidateOptions {
 
 export class Consolidator {
   private client: Anthropic | null = null;
+  private cachedApiKey: string | null = null;
   private db: EngramDatabase;
   private graph: KnowledgeGraph | null = null;
   private search: HybridSearch | null = null;
@@ -125,14 +126,36 @@ export class Consolidator {
     this.graph = graph || null;
     this.search = search || null;
 
+    // Initial check
+    this.ensureClient();
+  }
+
+  /**
+   * Ensure client is configured with latest API key
+   * Lazy initialization: checks for new/updated API key each call
+   */
+  private ensureClient(): Anthropic | null {
     const apiKey = getAnthropicApiKey();
-    if (apiKey) {
+
+    if (!apiKey) {
+      this.client = null;
+      this.cachedApiKey = null;
+      return null;
+    }
+
+    // Only recreate client if API key changed
+    if (apiKey !== this.cachedApiKey) {
+      console.error(`[Engram] Consolidator: API key ${this.cachedApiKey ? "updated" : "configured"}`);
       this.client = new Anthropic({ apiKey });
+      this.cachedApiKey = apiKey;
     }
+
+    return this.client;
   }
 
   isConfigured(): boolean {
-    return this.client !== null;
+    // Re-check in case API key was added after startup
+    return this.ensureClient() !== null;
   }
 
   /**
@@ -144,7 +167,8 @@ export class Consolidator {
     contradictionsFound: number;
     memoriesProcessed: number;
   }> {
-    if (!this.client) {
+    const client = this.ensureClient();
+    if (!client) {
       throw new Error("Consolidator not configured - set ANTHROPIC_API_KEY");
     }
 
@@ -221,7 +245,8 @@ export class Consolidator {
   private async consolidateBatch(
     memories: Memory[]
   ): Promise<ConsolidationResult | null> {
-    if (!this.client) return null;
+    const client = this.ensureClient();
+    if (!client) return null;
 
     // Format memories for the prompt
     const memoriesText = memories
@@ -246,7 +271,7 @@ ${memoriesText}
 Create a detailed digest that preserves all important information. Respond with JSON only.`;
 
     try {
-      const response = await this.client.messages.create({
+      const response = await client.messages.create({
         model: "claude-opus-4-5-20251101",
         max_tokens: 16000,
         temperature: 1, // Required for extended thinking
@@ -290,7 +315,8 @@ Create a detailed digest that preserves all important information. Respond with
    * Create an entity profile by consolidating all observations about an entity
    */
   async consolidateEntity(entityId: string): Promise<Digest | null> {
-    if (!this.client) {
+    const client = this.ensureClient();
+    if (!client) {
       throw new Error("Consolidator not configured - set ANTHROPIC_API_KEY");
     }
 
@@ -335,7 +361,7 @@ ${memoriesText}
 Create a rich, detailed profile. Do not summarize away important nuances. Respond with JSON only.`;
 
     try {
-      const response = await this.client.messages.create({
+      const response = await client.messages.create({
         model: "claude-opus-4-5-20251101",
         max_tokens: 16000,
         temperature: 1, // Required for extended thinking
@@ -444,7 +470,8 @@ Create a rich, detailed profile. Do not summarize away important nuances. Respon
     memoriesCreated: number;
     entitiesCreated: number;
   }> {
-    if (!this.client) {
+    const client = this.ensureClient();
+    if (!client) {
       throw new Error("Consolidator not configured - set ANTHROPIC_API_KEY");
     }
 
@@ -537,7 +564,8 @@ Create a rich, detailed profile. Do not summarize away important nuances. Respon
   private async extractMemoriesFromEpisodes(
     episodes: Episode[]
   ): Promise<EpisodeExtractionResult | null> {
-    if (!this.client) return null;
+    const client = this.ensureClient();
+    if (!client) return null;
 
     // Format conversation
     const conversationText = episodes
@@ -555,7 +583,7 @@ Respond with JSON only.`;
 
     try {
       // Use Haiku for speed/cost (no extended thinking needed)
-      const response = await this.client.messages.create({
+      const response = await client.messages.create({
         model: "claude-haiku-4-5-20251201",
         max_tokens: 4000,
         messages: [

package/src/index.ts

@@ -14,6 +14,7 @@ import {
 } from "@modelcontextprotocol/sdk/types.js";
 import path from "path";
 import os from "os";
+import fs from "fs";
 
 import { EngramDatabase } from "./storage/database.js";
 import { KnowledgeGraph } from "./graph/knowledge-graph.js";
@@ -29,6 +30,99 @@ const DB_PATH = process.env.ENGRAM_DB_PATH
   : path.join(os.homedir(), ".engram");
 
 const DB_FILE = path.join(DB_PATH, "engram.db");
+const PID_FILE = path.join(DB_PATH, "engram.pid");
+
+// ============ Zombie Prevention ============
+
+/**
+ * Kill any existing engram process and clean up stale PID file
+ */
+function cleanupZombies(): void {
+  try {
+    if (fs.existsSync(PID_FILE)) {
+      const oldPid = parseInt(fs.readFileSync(PID_FILE, "utf-8").trim(), 10);
+      if (oldPid && oldPid !== process.pid) {
+        try {
+          // Check if process exists
+          process.kill(oldPid, 0);
+          // It exists, kill it
+          console.error(`[Engram] Killing old instance (PID ${oldPid})`);
+          process.kill(oldPid, "SIGTERM");
+        } catch {
+          // Process doesn't exist, that's fine
+        }
+      }
+      fs.unlinkSync(PID_FILE);
+    }
+  } catch (error) {
+    console.error("[Engram] Error cleaning up zombies:", error);
+  }
+}
+
+/**
+ * Write our PID file
+ */
+function writePidFile(): void {
+  try {
+    // Ensure directory exists
+    if (!fs.existsSync(DB_PATH)) {
+      fs.mkdirSync(DB_PATH, { recursive: true });
+    }
+    fs.writeFileSync(PID_FILE, String(process.pid));
+  } catch (error) {
+    console.error("[Engram] Error writing PID file:", error);
+  }
+}
+
+/**
+ * Clean up on exit
+ */
+function cleanup(): void {
+  try {
+    if (fs.existsSync(PID_FILE)) {
+      const storedPid = parseInt(fs.readFileSync(PID_FILE, "utf-8").trim(), 10);
+      if (storedPid === process.pid) {
+        fs.unlinkSync(PID_FILE);
+      }
+    }
+    if (webServer) {
+      webServer.stop();
+    }
+    if (db) {
+      db.close();
+    }
+  } catch {
+    // Ignore cleanup errors
+  }
+}
+
+// Register signal handlers early
+process.on("SIGTERM", () => {
+  console.error("[Engram] Received SIGTERM, shutting down...");
+  cleanup();
+  process.exit(0);
+});
+
+process.on("SIGINT", () => {
+  console.error("[Engram] Received SIGINT, shutting down...");
+  cleanup();
+  process.exit(0);
+});
+
+process.on("exit", cleanup);
+
+// Detect when parent process (Claude) dies by monitoring stdin
+process.stdin.on("end", () => {
+  console.error("[Engram] stdin closed, parent process likely died. Shutting down...");
+  cleanup();
+  process.exit(0);
+});
+
+process.stdin.on("close", () => {
+  console.error("[Engram] stdin closed, shutting down...");
+  cleanup();
+  process.exit(0);
+});
 
 // ============ Initialize Components ============
 
@@ -624,17 +718,44 @@ server.setRequestHandler(CallToolRequestSchema, async (request) => {
           need_more?: boolean;
         };
 
-        // Update the retrieval log with feedback
-        const updated = db.updateRetrievalFeedback(recall_id, useful_memory_ids, need_more);
+        // First, get the original recall to validate useful_memory_ids
+        const retrievalLog = db.getRetrievalLog(recall_id);
+        if (!retrievalLog) {
+          return {
+            content: [
+              {
+                type: "text" as const,
+                text: JSON.stringify({
+                  success: false,
+                  error: `Recall ID not found: ${recall_id}`,
+                }),
+              },
+            ],
+          };
+        }
+
+        // Validate: only accept IDs that were in the original recall
+        const originalIdSet = new Set(retrievalLog.memory_ids);
+        const validUsefulIds = useful_memory_ids.filter(id => originalIdSet.has(id));
+        const invalidIds = useful_memory_ids.filter(id => !originalIdSet.has(id));
+
+        if (invalidIds.length > 0) {
+          console.error(`[Engram] memory_feedback: ${invalidIds.length} IDs not in original recall, ignored: ${invalidIds.join(", ")}`);
+        }
+
+        // Update the retrieval log with validated feedback
+        const updated = db.updateRetrievalFeedback(recall_id, validUsefulIds, need_more);
 
         if (!updated) {
+          // Should not happen since we already checked above, but handle gracefully
+          console.error(`[Engram] memory_feedback: failed to update retrieval log ${recall_id}`);
           return {
             content: [
               {
                 type: "text" as const,
                 text: JSON.stringify({
                   success: false,
-                  error: `Recall ID not found: ${recall_id}`,
+                  error: `Failed to update feedback for: ${recall_id}`,
                 }),
               },
             ],
@@ -664,7 +785,7 @@ server.setRequestHandler(CallToolRequestSchema, async (request) => {
                 text: JSON.stringify({
                   success: true,
                   feedback_recorded: true,
-                  useful_count: useful_memory_ids.length,
+                  useful_count: validUsefulIds.length,
                   expanded_search: true,
                   additional_results: formatted,
                   additional_count: formatted.length,
@@ -697,7 +818,7 @@ server.setRequestHandler(CallToolRequestSchema, async (request) => {
               text: JSON.stringify({
                 success: true,
                 feedback_recorded: true,
-                useful_count: useful_memory_ids.length,
+                useful_count: validUsefulIds.length,
                 learning_applied: learningApplied > 0,
                 connections_strengthened: learningApplied,
               }, null, 2),
@@ -726,12 +847,16 @@ server.setRequestHandler(CallToolRequestSchema, async (request) => {
 // ============ Main ============
 
 async function main() {
+  // Kill any zombie instances before starting
+  cleanupZombies();
+  writePidFile();
+
   await initialize();
 
   const transport = new StdioServerTransport();
   await server.connect(transport);
 
-  console.error("[Engram] MCP server running on stdio");
+  console.error(`[Engram] MCP server running on stdio (PID ${process.pid})`);
 }
 
 main().catch((error) => {

package/src/retrieval/hybrid.ts

@@ -327,8 +327,12 @@ export class HybridSearch {
     // Log this retrieval for deferred learning
     try {
       this.db.createRetrievalLog(this.sessionId, recallId, query, allResultIds);
-    } catch {
-      // Ignore duplicate recall_id errors (can happen with rapid queries)
+    } catch (error) {
+      // Only ignore duplicate recall_id errors (UNIQUE constraint), log all others
+      const msg = error instanceof Error ? error.message : String(error);
+      if (!msg.includes("UNIQUE constraint")) {
+        console.error(`[Engram] Failed to create retrieval log: ${msg}`);
+      }
     }
 
     return {

package/src/storage/database.ts

@@ -1183,59 +1183,72 @@ export class EngramDatabase {
 
   /**
    * Record that memories were retrieved together (co-retrieval)
+   * Uses cached statement and transaction for O(n²) efficiency
    */
   recordCoRetrieval(memoryIds: string[]): void {
     if (memoryIds.length < 2) return;
 
-    // Update all pairs
-    for (let i = 0; i < memoryIds.length; i++) {
-      for (let j = i + 1; j < memoryIds.length; j++) {
-        const [a, b] = memoryIds[i] < memoryIds[j]
-          ? [memoryIds[i], memoryIds[j]]
-          : [memoryIds[j], memoryIds[i]];
-
-        this.db.prepare(`
-          INSERT INTO memory_connections (id, memory_a, memory_b, co_retrievals, last_fired)
-          VALUES (?, ?, ?, 1, CURRENT_TIMESTAMP)
-          ON CONFLICT(memory_a, memory_b) DO UPDATE SET
-            co_retrievals = co_retrievals + 1,
-            last_fired = CURRENT_TIMESTAMP
-        `).run(randomUUID(), a, b);
+    // Cache statement once (not per iteration)
+    const upsertStmt = this.stmt(`
+      INSERT INTO memory_connections (id, memory_a, memory_b, co_retrievals, last_fired)
+      VALUES (?, ?, ?, 1, CURRENT_TIMESTAMP)
+      ON CONFLICT(memory_a, memory_b) DO UPDATE SET
+        co_retrievals = co_retrievals + 1,
+        last_fired = CURRENT_TIMESTAMP
+    `);
+
+    // Wrap in transaction for batch efficiency
+    this.db.transaction(() => {
+      for (let i = 0; i < memoryIds.length; i++) {
+        for (let j = i + 1; j < memoryIds.length; j++) {
+          const [a, b] = memoryIds[i] < memoryIds[j]
+            ? [memoryIds[i], memoryIds[j]]
+            : [memoryIds[j], memoryIds[i]];
+
+          upsertStmt.run(randomUUID(), a, b);
+        }
       }
-    }
+    })();
   }
 
   /**
    * Record that memories were useful together (from LLM feedback)
    * This is what actually strengthens connections
+   * Uses cached statement and transaction for O(n²) efficiency
    */
   recordCoUseful(memoryIds: string[]): void {
     if (memoryIds.length < 2) return;
 
-    for (let i = 0; i < memoryIds.length; i++) {
-      for (let j = i + 1; j < memoryIds.length; j++) {
-        const [a, b] = memoryIds[i] < memoryIds[j]
-          ? [memoryIds[i], memoryIds[j]]
-          : [memoryIds[j], memoryIds[i]];
-
-        // Get current stats to calculate new strength
-        const conn = this.getOrCreateConnection(a, b);
-        const newCoUseful = conn.co_useful + 1;
-        const newCoRetrievals = Math.max(conn.co_retrievals, newCoUseful);
-
-        // Calculate strength with diminishing returns
-        const usefulRatio = newCoUseful / Math.max(1, newCoRetrievals);
-        const diminished = Math.sqrt(usefulRatio);
-        const confidence = Math.min(1, newCoUseful / 3); // Require 3+ co-useful for strong connection
-        const newStrength = diminished * confidence;
-
-        this.db.prepare(`
-          UPDATE memory_connections
-          SET co_useful = ?, strength = ?, last_fired = CURRENT_TIMESTAMP
-          WHERE memory_a = ? AND memory_b = ?
-        `).run(newCoUseful, newStrength, a, b);
+    // Cache statement once (not per iteration)
+    const updateStmt = this.stmt(`
+      UPDATE memory_connections
+      SET co_useful = ?, strength = ?, last_fired = CURRENT_TIMESTAMP
+      WHERE memory_a = ? AND memory_b = ?
+    `);
+
+    // Wrap in transaction for batch efficiency
+    this.db.transaction(() => {
+      for (let i = 0; i < memoryIds.length; i++) {
+        for (let j = i + 1; j < memoryIds.length; j++) {
+          const [a, b] = memoryIds[i] < memoryIds[j]
+            ? [memoryIds[i], memoryIds[j]]
+            : [memoryIds[j], memoryIds[i]];
+
+          // Get current stats to calculate new strength
+          const conn = this.getOrCreateConnection(a, b);
+          const newCoUseful = conn.co_useful + 1;
+          const newCoRetrievals = Math.max(conn.co_retrievals, newCoUseful);
+
+          // Calculate strength with diminishing returns
+          const usefulRatio = newCoUseful / Math.max(1, newCoRetrievals);
+          const diminished = Math.sqrt(usefulRatio);
+          const confidence = Math.min(1, newCoUseful / 3); // Require 3+ co-useful for strong connection
+          const newStrength = diminished * confidence;
+
+          updateStmt.run(newCoUseful, newStrength, a, b);
+        }
       }
-    }
+    })();
   }
 
   /**

package/src/web/chat-handler.ts

@@ -1,6 +1,6 @@
 /**
  * Chat Handler for Engram Web Interface
- * Uses Claude Haiku 4.5 with tools for entity/memory management
+ * Uses Claude Opus 4.5 with tools for entity/memory management
  */
 
 import Anthropic from "@anthropic-ai/sdk";
@@ -9,22 +9,22 @@ import { KnowledgeGraph } from "../graph/knowledge-graph.js";
 import { HybridSearch } from "../retrieval/hybrid.js";
 import { getAnthropicApiKey } from "../settings.js";
 
-// Tool definitions for Claude
+// Tool definitions for Claude - optimized for LLM consumption
 const TOOLS: Anthropic.Tool[] = [
   {
     name: "list_entities",
-    description: "List all entities in the knowledge graph. Use this to see what people, organizations, and places are stored.",
+    description: "Returns array of {name, type, id}. Filters: type (person|organization|place), limit. Default limit=50.",
     input_schema: {
       type: "object" as const,
       properties: {
         type: {
           type: "string",
           enum: ["person", "organization", "place"],
-          description: "Filter by entity type (optional)",
+          description: "Filter: person, organization, or place",
         },
         limit: {
-          type: "number",
-          description: "Maximum number of entities to return (default: 50)",
+          type: "integer",
+          description: "Max results (default: 50)",
         },
       },
       required: [],
@@ -32,13 +32,13 @@ const TOOLS: Anthropic.Tool[] = [
   },
   {
     name: "get_entity",
-    description: "Get detailed information about an entity including its observations and relationships.",
+    description: "Returns {name, type, observations[], relationships_from[], relationships_to[]} or {error}.",
     input_schema: {
       type: "object" as const,
       properties: {
         name: {
           type: "string",
-          description: "The entity name to look up",
+          description: "Exact entity name (case-sensitive)",
         },
       },
       required: ["name"],
@@ -46,13 +46,13 @@ const TOOLS: Anthropic.Tool[] = [
   },
   {
     name: "delete_entity",
-    description: "Delete an entity and all its observations and relationships. Use this to remove incorrect or duplicate entities.",
+    description: "Permanently removes entity + all observations + all relationships. Returns {success, deleted} or {error}.",
     input_schema: {
       type: "object" as const,
       properties: {
         name: {
           type: "string",
-          description: "The entity name to delete",
+          description: "Exact entity name to delete",
         },
       },
       required: ["name"],
@@ -60,17 +60,17 @@ const TOOLS: Anthropic.Tool[] = [
   },
   {
     name: "merge_entities",
-    description: "Merge one entity into another. All observations and relationships from the source will be moved to the target, then the source is deleted. Use this to fix duplicates.",
+    description: "Moves all data from 'merge' into 'keep', then deletes 'merge'. Use for deduplication. Returns {success, kept, merged, observations_moved, relations_moved} or {error}.",
     input_schema: {
       type: "object" as const,
       properties: {
         keep: {
           type: "string",
-          description: "The entity name to keep (target)",
+          description: "Entity name to preserve (target)",
         },
         merge: {
           type: "string",
-          description: "The entity name to merge and delete (source)",
+          description: "Entity name to merge then delete (source)",
         },
       },
       required: ["keep", "merge"],
@@ -78,17 +78,17 @@ const TOOLS: Anthropic.Tool[] = [
   },
   {
     name: "rename_entity",
-    description: "Rename an entity to a new name.",
+    description: "Changes entity name. Returns {success, old_name, new_name} or {error}.",
     input_schema: {
       type: "object" as const,
       properties: {
         old_name: {
           type: "string",
-          description: "Current entity name",
+          description: "Current exact name",
         },
         new_name: {
           type: "string",
-          description: "New entity name",
+          description: "New name",
         },
       },
       required: ["old_name", "new_name"],
@@ -96,7 +96,7 @@ const TOOLS: Anthropic.Tool[] = [
   },
   {
     name: "delete_relationship",
-    description: "Delete a relationship between two entities.",
+    description: "Removes specific relationship. All 3 params must match exactly. Returns {success, deleted} or {error}.",
     input_schema: {
       type: "object" as const,
       properties: {
@@ -110,7 +110,7 @@ const TOOLS: Anthropic.Tool[] = [
         },
         type: {
           type: "string",
-          description: "Relationship type (e.g., 'works_at', 'knows')",
+          description: "Relationship type (e.g., works_at, knows, lives_in)",
         },
       },
       required: ["from", "to", "type"],
@@ -118,17 +118,17 @@ const TOOLS: Anthropic.Tool[] = [
   },
   {
     name: "search_memories",
-    description: "Search through stored memories.",
+    description: "Hybrid BM25+semantic search. Returns {results[{id, content, timestamp, score}], count}.",
     input_schema: {
       type: "object" as const,
       properties: {
         query: {
           type: "string",
-          description: "Search query",
+          description: "Search query (keywords or natural language)",
         },
         limit: {
-          type: "number",
-          description: "Maximum results (default: 10)",
+          type: "integer",
+          description: "Max results (default: 10)",
         },
       },
       required: ["query"],
@@ -136,13 +136,13 @@ const TOOLS: Anthropic.Tool[] = [
   },
   {
     name: "delete_memory",
-    description: "Delete a memory by its ID (soft-delete, can be recovered).",
+    description: "Soft-delete (recoverable). Returns {success, disabled_id} or {error}.",
     input_schema: {
       type: "object" as const,
       properties: {
         id: {
           type: "string",
-          description: "The memory ID to delete",
+          description: "Memory UUID",
         },
       },
       required: ["id"],
@@ -150,13 +150,13 @@ const TOOLS: Anthropic.Tool[] = [
   },
   {
     name: "edit_memory",
-    description: "Edit an existing memory's content or importance.",
+    description: "Updates content and/or importance. Returns {success, memory_id, updated_fields[]} or {error}.",
     input_schema: {
       type: "object" as const,
       properties: {
         id: {
           type: "string",
-          description: "The memory ID to edit",
+          description: "Memory UUID",
         },
         content: {
           type: "string",
@@ -164,7 +164,9 @@ const TOOLS: Anthropic.Tool[] = [
         },
         importance: {
           type: "number",
-          description: "New importance (0-1): 0.9=core identity, 0.8=major, 0.5=normal, 0.3=minor",
+          minimum: 0,
+          maximum: 1,
+          description: "0-1: 0.9=identity, 0.8=major, 0.5=normal, 0.3=minor",
         },
       },
       required: ["id"],
@@ -172,17 +174,19 @@ const TOOLS: Anthropic.Tool[] = [
   },
   {
     name: "create_memory",
-    description: "Create a new memory. Use for storing user information, preferences, or facts.",
+    description: "Stores new memory. Returns {success, memory_id, content}.",
     input_schema: {
       type: "object" as const,
       properties: {
         content: {
           type: "string",
-          description: "The information to store",
+          description: "Information to store",
         },
         importance: {
           type: "number",
-          description: "0-1 score: 0.9=core identity, 0.8=major, 0.5=normal (default), 0.3=minor",
+          minimum: 0,
+          maximum: 1,
+          description: "0-1: 0.9=identity, 0.8=major, 0.5=normal (default), 0.3=minor",
         },
       },
       required: ["content"],
@@ -190,13 +194,13 @@ const TOOLS: Anthropic.Tool[] = [
   },
   {
     name: "create_entity",
-    description: "Create a new entity (person, organization, or place).",
+    description: "Creates new entity. Returns {success, entity_id, name, type} or {error} if exists.",
     input_schema: {
       type: "object" as const,
       properties: {
         name: {
           type: "string",
-          description: "The entity name",
+          description: "Entity name",
         },
         type: {
           type: "string",
@@ -209,7 +213,7 @@ const TOOLS: Anthropic.Tool[] = [
   },
   {
     name: "create_relationship",
-    description: "Create a relationship between two entities.",
+    description: "Links two entities. Auto-creates entities as 'person' if missing. Returns {success, relationship}.",
     input_schema: {
       type: "object" as const,
       properties: {
@@ -223,7 +227,7 @@ const TOOLS: Anthropic.Tool[] = [
         },
         type: {
           type: "string",
-          description: "Relationship type (e.g., 'works_at', 'lives_in', 'knows', 'sibling_of')",
+          description: "Relationship type (e.g., works_at, lives_in, knows, sibling_of, parent_of)",
         },
       },
       required: ["from", "to", "type"],
@@ -231,7 +235,7 @@ const TOOLS: Anthropic.Tool[] = [
   },
   {
     name: "find_duplicates",
-    description: "Find potential duplicate entities that could be merged.",
+    description: "Detects similar entity names. Returns {groups[{keep, duplicates[]}], total_duplicates}.",
     input_schema: {
       type: "object" as const,
       properties: {},
@@ -240,7 +244,7 @@ const TOOLS: Anthropic.Tool[] = [
   },
   {
     name: "auto_tidy",
-    description: "Automatically merge all detected duplicate entities.",
+    description: "Auto-merges all detected duplicates. Returns {entities_merged, observations_moved, relations_moved}.",
     input_schema: {
       type: "object" as const,
       properties: {},
@@ -301,6 +305,9 @@ export class ChatHandler {
   refreshClient(): void {
     const apiKey = getAnthropicApiKey();
     if (apiKey) {
+      if (!this.client) {
+        console.error("[Engram] ChatHandler: API key configured");
+      }
       this.client = new Anthropic({ apiKey });
     } else {
       this.client = null;
@@ -308,6 +315,8 @@ export class ChatHandler {
   }
 
   isConfigured(): boolean {
+    // Re-check API key in case it was added after startup
+    this.refreshClient();
     return this.client !== null;
   }
 
@@ -341,6 +350,7 @@ export class ChatHandler {
 
   // Queue-aware chat method
   async chat(userMessage: string): Promise<string> {
+    this.refreshClient();
     if (!this.client) {
       return "Chat is not configured. Set ANTHROPIC_API_KEY environment variable.";
     }
@@ -357,6 +367,7 @@ export class ChatHandler {
 
   // Streaming chat with callbacks for real-time updates
   async *chatStream(userMessage: string): AsyncGenerator<StreamEvent> {
+    this.refreshClient();
     if (!this.client) {
       yield { type: "error", content: "Chat is not configured. Set ANTHROPIC_API_KEY environment variable." };
       return;
@@ -377,11 +388,10 @@ export class ChatHandler {
       }
 
       let continueLoop = true;
-      let fullResponse = "";
 
       while (continueLoop) {
         const stream = this.client.messages.stream({
-          model: "claude-haiku-4-5-20241022",
+          model: "claude-opus-4-5-20251101",
           max_tokens: 1024,
           system: SYSTEM_PROMPT,
           tools: TOOLS,
@@ -402,25 +412,13 @@ export class ChatHandler {
             }
           } else if (event.type === "content_block_delta") {
             if (event.delta.type === "text_delta") {
-              fullResponse += event.delta.text;
               yield { type: "text", content: event.delta.text };
             } else if (event.delta.type === "input_json_delta" && currentToolUse) {
               currentToolUse.input += event.delta.partial_json;
             }
           } else if (event.type === "content_block_stop") {
-            if (currentToolUse) {
-              // Execute the tool
-              let toolInput: Record<string, unknown> = {};
-              try {
-                toolInput = JSON.parse(currentToolUse.input || "{}");
-              } catch {
-                toolInput = {};
-              }
-
-              const result = await this.executeTool(currentToolUse.name, toolInput);
-              yield { type: "tool_end", tool: currentToolUse.name, result };
-              currentToolUse = null;
-            }
+            // Don't execute tools here - wait for finalMessage to avoid double execution
+            currentToolUse = null;
           }
         }
 
@@ -428,7 +426,7 @@ export class ChatHandler {
         const finalMessage = await stream.finalMessage();
 
         if (finalMessage.stop_reason === "tool_use") {
-          // Process tool results and continue
+          // Process tool results (execute only once, here)
           const toolUseBlocks = finalMessage.content.filter(
             (block): block is Anthropic.ToolUseBlock => block.type === "tool_use"
           );
@@ -436,10 +434,13 @@ export class ChatHandler {
           const toolResults: Anthropic.ToolResultBlockParam[] = [];
           for (const toolUse of toolUseBlocks) {
             const result = await this.executeTool(toolUse.name, toolUse.input as Record<string, unknown>);
+            const isError = typeof result === "object" && result !== null && "error" in result;
+            yield { type: "tool_end", tool: toolUse.name, result };
             toolResults.push({
               type: "tool_result",
               tool_use_id: toolUse.id,
               content: JSON.stringify(result),
+              is_error: isError,
             });
           }
 
@@ -492,7 +493,7 @@ export class ChatHandler {
       }
 
       let response = await this.client.messages.create({
-        model: "claude-haiku-4-5-20241022",
+        model: "claude-opus-4-5-20251101",
         max_tokens: 1024,
         system: SYSTEM_PROMPT,
         tools: TOOLS,
@@ -508,10 +509,12 @@ export class ChatHandler {
         const toolResults: Anthropic.ToolResultBlockParam[] = [];
         for (const toolUse of toolUseBlocks) {
           const result = await this.executeTool(toolUse.name, toolUse.input as Record<string, unknown>);
+          const isError = typeof result === "object" && result !== null && "error" in result;
           toolResults.push({
             type: "tool_result",
             tool_use_id: toolUse.id,
             content: JSON.stringify(result),
+            is_error: isError,
           });
         }
 
@@ -527,7 +530,7 @@ export class ChatHandler {
 
         // Continue the conversation
         response = await this.client.messages.create({
-          model: "claude-haiku-4-5-20241022",
+          model: "claude-opus-4-5-20251101",
           max_tokens: 1024,
           system: SYSTEM_PROMPT,
           tools: TOOLS,