@aeriondyseti/vector-memory-mcp 2.3.0 → 2.4.4-dev.1

package/server/core/memory.service.ts

@@ -1,17 +1,19 @@
 import { randomUUID, createHash } from "crypto";
-import type { Memory, SearchIntent, IntentProfile, HybridRow } from "./memory.js";
-import { isDeleted } from "./memory.js";
-import type { SearchResult, SearchOptions } from "./conversation.js";
-import type { MemoryRepository } from "./memory.repository.js";
-import type { EmbeddingsService } from "./embeddings.service.js";
-import type { ConversationHistoryService } from "./conversation.service.js";
-
+import type { Memory, SearchIntent, IntentProfile, HybridRow } from "./memory";
+import { isDeleted, computeConfidence } from "./memory";
+import type { SearchResult, SearchOptions } from "./conversation";
+import type { MemoryRepository } from "./memory.repository";
+import type { EmbeddingsService } from "./embeddings.service";
+import type { ConversationHistoryService } from "./conversation.service";
+
+// Jitter values halved from original (0.02/0.05/0.15) because RRF_K=10 produces
+// ~6x more score spread than K=60, amplifying jitter's disruption effect.
 const INTENT_PROFILES: Record<SearchIntent, IntentProfile> = {
-  continuity: { weights: { relevance: 0.3, recency: 0.5, utility: 0.2 }, jitter: 0.02 },
-  fact_check: { weights: { relevance: 0.6, recency: 0.1, utility: 0.3 }, jitter: 0.02 },
-  frequent: { weights: { relevance: 0.2, recency: 0.2, utility: 0.6 }, jitter: 0.02 },
-  associative: { weights: { relevance: 0.7, recency: 0.1, utility: 0.2 }, jitter: 0.05 },
-  explore: { weights: { relevance: 0.4, recency: 0.3, utility: 0.3 }, jitter: 0.15 },
+  continuity: { weights: { relevance: 0.3, recency: 0.5, utility: 0.2 }, jitter: 0.01 },
+  fact_check: { weights: { relevance: 0.6, recency: 0.1, utility: 0.3 }, jitter: 0.01 },
+  frequent: { weights: { relevance: 0.2, recency: 0.2, utility: 0.6 }, jitter: 0.01 },
+  associative: { weights: { relevance: 0.7, recency: 0.1, utility: 0.2 }, jitter: 0.025 },
+  explore: { weights: { relevance: 0.4, recency: 0.3, utility: 0.3 }, jitter: 0.08 },
 };
 
 const sigmoid = (x: number): number => 1 / (1 + Math.exp(-x));
@@ -87,19 +89,10 @@ export class MemoryService {
   async getMultiple(ids: string[]): Promise<Memory[]> {
     if (ids.length === 0) return [];
     const memories = await this.repository.findByIds(ids);
-    // Track access in bulk
     const now = new Date();
-    const live = memories.filter((m) => !isDeleted(m));
-    await Promise.all(
-      live.map((m) =>
-        this.repository.upsert({
-          ...m,
-          accessCount: m.accessCount + 1,
-          lastAccessed: now,
-        })
-      )
-    );
-    return live;
+    const liveIds = memories.filter((m) => !isDeleted(m)).map((m) => m.id);
+    this.repository.bulkUpdateAccess(liveIds, now);
+    return memories.filter((m) => !isDeleted(m));
   }
 
   async delete(id: string): Promise<boolean> {
@@ -186,10 +179,10 @@ export class MemoryService {
   async search(
     query: string,
     intent: SearchIntent,
-    limit: number = 10,
-    includeDeleted: boolean = false,
     options?: SearchOptions
   ): Promise<SearchResult[]> {
+    const limit = options?.limit ?? 10;
+    const includeDeleted = options?.includeDeleted ?? false;
     const queryEmbedding = await this.embeddings.embed(query);
     const profile = INTENT_PROFILES[intent];
     const now = new Date();
@@ -223,6 +216,7 @@ export class MemoryService {
                   updatedAt: candidate.updatedAt,
                   source: "memory" as const,
                   score: this.computeMemoryScore(candidate, profile, now),
+                  confidence: computeConfidence(candidate.signals),
                   supersededBy: candidate.supersededBy,
                   usefulness: candidate.usefulness,
                   accessCount: candidate.accessCount,
@@ -249,6 +243,7 @@ export class MemoryService {
                 updatedAt: row.createdAt,
                 source: "conversation_history" as const,
                 score: row.rrfScore * historyWeight,
+                confidence: computeConfidence(row.signals),
                 supersededBy: null,
                 sessionId: (row.metadata?.session_id as string) ?? "",
                 role: (row.metadata?.role as string) ?? "unknown",
@@ -272,19 +267,7 @@ export class MemoryService {
 
   async trackAccess(ids: string[]): Promise<void> {
     if (ids.length === 0) return;
-    const memories = await this.repository.findByIds(ids);
-    const now = new Date();
-    await Promise.all(
-      memories
-        .filter((m) => !isDeleted(m))
-        .map((m) =>
-          this.repository.upsert({
-            ...m,
-            accessCount: m.accessCount + 1,
-            lastAccessed: now,
-          })
-        )
-    );
+    this.repository.bulkUpdateAccess(ids, new Date());
   }
 
   private static readonly UUID_ZERO =
@@ -292,8 +275,16 @@ export class MemoryService {
 
   private static waypointId(project?: string): string {
     if (!project?.length) return MemoryService.UUID_ZERO;
-    const hex = createHash("sha256").update(`waypoint:${project}`).digest("hex");
-    // Format as UUID: 8-4-4-4-12
+    const normalized = project.trim().toLowerCase();
+    const hex = createHash("sha256").update(`waypoint:${normalized}`).digest("hex");
+    return `wp:${hex.slice(0, 32)}`;
+  }
+
+  /** Legacy UUID-formatted waypoint ID for migration fallback reads. */
+  private static legacyWaypointId(project?: string): string | null {
+    if (!project?.length) return null; // UUID_ZERO is still current for no-project
+    const normalized = project.trim().toLowerCase();
+    const hex = createHash("sha256").update(`waypoint:${normalized}`).digest("hex");
     return [
       hex.slice(0, 8),
       hex.slice(8, 12),
@@ -386,6 +377,20 @@ ${list(args.memory_ids)}`;
   }
 
   async getLatestWaypoint(project?: string): Promise<Memory | null> {
-    return await this.get(MemoryService.waypointId(project));
+    const waypoint = await this.get(MemoryService.waypointId(project));
+    if (waypoint) return waypoint;
+
+    // Fallback: try legacy UUID-formatted waypoint ID and migrate on read
+    const legacyId = MemoryService.legacyWaypointId(project);
+    if (!legacyId) return null;
+
+    const legacy = await this.repository.findById(legacyId);
+    if (!legacy) return null;
+
+    // Migrate: write under new ID, delete old
+    const newId = MemoryService.waypointId(project);
+    await this.repository.upsert({ ...legacy, id: newId });
+    await this.repository.markDeleted(legacyId);
+    return { ...legacy, id: newId };
   }
 }

package/server/core/memory.ts

@@ -38,7 +38,46 @@ export interface IntentProfile {
   jitter: number;
 }
 
+/** Signals preserved from the hybrid search pipeline for confidence scoring. */
+export interface SearchSignals {
+  cosineSimilarity: number | null;
+  ftsMatch: boolean;
+  knnRank: number | null;
+  ftsRank: number | null;
+}
+
 /** Augments any entity type with an RRF score from hybrid search. */
-export type WithRrfScore<T> = T & { rrfScore: number };
+export type WithRrfScore<T> = T & { rrfScore: number; signals: SearchSignals };
 
 export type HybridRow = WithRrfScore<Memory>;
+
+/**
+ * Compute absolute confidence (0-1) from search signals.
+ *
+ * Based primarily on cosine similarity (the strongest absolute signal)
+ * mapped through a sigmoid with an agreement bonus for dual-path matches.
+ * The midpoint and steepness are calibrated for all-MiniLM-L6-v2 embeddings.
+ */
+// Calibrated against all-MiniLM-L6-v2: noise ceiling ~0.25, weak-relevant floor ~0.30
+const CONFIDENCE_STEEPNESS = 14;
+const CONFIDENCE_MIDPOINT = 0.35;
+const CONFIDENCE_AGREEMENT_BONUS = 0.08;
+
+export function computeConfidence(signals: SearchSignals): number {
+  const sim = signals.cosineSimilarity;
+
+  if (sim === null) {
+    // FTS-only result — keyword match but no semantic confirmation
+    return signals.ftsMatch ? 0.40 : 0.0;
+  }
+
+  // Shifted sigmoid: maps cosine similarity to interpretable confidence
+  let confidence = 1 / (1 + Math.exp(-CONFIDENCE_STEEPNESS * (sim - CONFIDENCE_MIDPOINT)));
+
+  // Dual-path agreement bonus: found by both KNN and FTS
+  if (signals.ftsMatch) {
+    confidence = Math.min(1.0, confidence + CONFIDENCE_AGREEMENT_BONUS);
+  }
+
+  return confidence;
+}

package/server/core/migration.service.ts

@@ -3,9 +3,9 @@ import { createHash } from "crypto";
 import { existsSync, statSync, readdirSync } from "fs";
 import { resolve, dirname } from "path";
 import { fileURLToPath } from "url";
-import { serializeVector } from "./sqlite-utils.js";
-import type { MemoryRepository } from "./memory.repository.js";
-import type { EmbeddingsService } from "./embeddings.service.js";
+import { serializeVector } from "./sqlite-utils";
+import type { MemoryRepository } from "./memory.repository";
+import type { EmbeddingsService } from "./embeddings.service";
 
 const __dirname = dirname(fileURLToPath(import.meta.url));
 

package/server/core/migrations.ts

@@ -1,6 +1,6 @@
 import type { Database } from "bun:sqlite";
-import type { EmbeddingsService } from "./embeddings.service.js";
-import { serializeVector } from "./sqlite-utils.js";
+import type { EmbeddingsService } from "./embeddings.service";
+import { serializeVector } from "./sqlite-utils";
 
 /**
  * Pre-migration step: remove vec0 virtual table entries from sqlite_master
@@ -127,8 +127,25 @@ export async function backfillVectors(
   db: Database,
   embeddings: EmbeddingsService,
 ): Promise<void> {
+  // Quick gap check: if no rows are missing vectors, skip the expensive backfill
+  const hasMemories = db.prepare("SELECT 1 FROM memories LIMIT 1").get();
+  const hasConvos = db.prepare("SELECT 1 FROM conversation_history LIMIT 1").get();
+
+  if (!hasMemories && !hasConvos) return;
+
+  const memoryGap = hasMemories && db.prepare(
+    `SELECT 1 FROM memories m LEFT JOIN memories_vec v ON m.id = v.id
+     WHERE v.id IS NULL OR length(v.vector) = 0 LIMIT 1`,
+  ).get();
+
+  const convoGap = hasConvos && db.prepare(
+    `SELECT 1 FROM conversation_history c LEFT JOIN conversation_history_vec v ON c.id = v.id
+     WHERE v.id IS NULL OR length(v.vector) = 0 LIMIT 1`,
+  ).get();
+
+  if (!memoryGap && !convoGap) return;
+
   // ── Memories ──────────────────────────────────────────────────────
-  // Catch both missing rows (v.id IS NULL) and corrupt 0-byte BLOBs
   const missingMemories = db
     .prepare(
       `SELECT m.id, m.content, json_extract(m.metadata, '$.type') AS type
@@ -151,14 +168,27 @@ export async function backfillVectors(
       new Array(embeddings.dimension).fill(0),
     );
 
-    for (const row of missingMemories) {
-      // Waypoints use a zero vector (not semantically searched)
-      const blob =
-        row.type === "waypoint"
-          ? zeroVector
-          : serializeVector(await embeddings.embed(row.content));
+    // Separate waypoints from content that needs embedding
+    const toEmbed = missingMemories.filter((r) => r.type !== "waypoint");
+    const waypoints = missingMemories.filter((r) => r.type === "waypoint");
 
-      insertVec.run(row.id, blob);
+    // Batch embed all non-waypoint content
+    const vectors = toEmbed.length > 0
+      ? await embeddings.embedBatch(toEmbed.map((r) => r.content))
+      : [];
+
+    db.exec("BEGIN");
+    try {
+      for (const row of waypoints) {
+        insertVec.run(row.id, zeroVector);
+      }
+      for (let i = 0; i < toEmbed.length; i++) {
+        insertVec.run(toEmbed[i].id, serializeVector(vectors[i]));
+      }
+      db.exec("COMMIT");
+    } catch (e) {
+      db.exec("ROLLBACK");
+      throw e;
     }
 
     console.error(
@@ -185,17 +215,27 @@ export async function backfillVectors(
       "INSERT OR REPLACE INTO conversation_history_vec (id, vector) VALUES (?, ?)",
     );
 
-    for (let i = 0; i < missingConvos.length; i++) {
-      const row = missingConvos[i];
-      const vec = serializeVector(await embeddings.embed(row.content));
-      insertConvoVec.run(row.id, vec);
-
-      // Log progress every 100 chunks
-      if ((i + 1) % 100 === 0) {
-        console.error(
-          `[vector-memory-mcp]   ...${i + 1}/${missingConvos.length} conversation chunks`,
-        );
+    // Batch embed in chunks of 32
+    const BATCH_SIZE = 32;
+    db.exec("BEGIN");
+    try {
+      for (let i = 0; i < missingConvos.length; i += BATCH_SIZE) {
+        const batch = missingConvos.slice(i, i + BATCH_SIZE);
+        const vecs = await embeddings.embedBatch(batch.map((r) => r.content));
+        for (let j = 0; j < batch.length; j++) {
+          insertConvoVec.run(batch[j].id, serializeVector(vecs[j]));
+        }
+
+        if ((i + BATCH_SIZE) % 100 < BATCH_SIZE) {
+          console.error(
+            `[vector-memory-mcp]   ...${Math.min(i + BATCH_SIZE, missingConvos.length)}/${missingConvos.length} conversation chunks`,
+          );
+        }
       }
+      db.exec("COMMIT");
+    } catch (e) {
+      db.exec("ROLLBACK");
+      throw e;
     }
 
     console.error(

package/server/core/parsers/claude-code.parser.ts

@@ -1,7 +1,7 @@
 import { readFile, readdir, stat } from "fs/promises";
 import { basename, dirname, join } from "path";
-import type { ParsedMessage, SessionFileInfo } from "../conversation.js";
-import type { SessionLogParser } from "./types.js";
+import type { ParsedMessage, SessionFileInfo } from "../conversation";
+import type { SessionLogParser } from "./types";
 
 // UUID pattern for session IDs
 const UUID_PATTERN =
@@ -45,7 +45,7 @@ export class ClaudeCodeSessionParser implements SessionLogParser {
     const fileName = basename(filePath, ".jsonl");
     const parentDir = basename(dirname(filePath));
     // Check if this is inside a subagents directory
-    const isSubagentFile = filePath.includes("/subagents/");
+    const isSubagentFile = /[/\\]subagents[/\\]/.test(filePath);
 
     // For subagent files, project dir is 3 levels up: <project>/<session>/subagents/<file>
     // For main files, project dir is direct parent

package/server/core/parsers/types.ts

@@ -1,4 +1,4 @@
-import type { ParsedMessage, SessionFileInfo } from "../conversation.js";
+import type { ParsedMessage, SessionFileInfo } from "../conversation";
 
 /** Interface for parsing session log files into structured messages */
 export interface SessionLogParser {

package/server/core/sqlite-utils.ts

@@ -1,7 +1,29 @@
 import type { Database } from "bun:sqlite";
 
-/** RRF constant matching the previous LanceDB reranker default */
-export const RRF_K = 60;
+/** RRF constant — lower K gives sharper top-rank discrimination in the 1/(K+rank) formula */
+export const RRF_K = 10;
+
+/**
+ * Maximum parameters per SQLite query to stay within SQLITE_MAX_VARIABLE_NUMBER.
+ */
+export const SQLITE_BATCH_SIZE = 100;
+
+/**
+ * Execute a query in batches when the number of parameters exceeds SQLITE_BATCH_SIZE.
+ * Splits the ids array and concatenates results.
+ */
+export function batchedQuery<T>(
+  db: Database,
+  ids: string[],
+  queryFn: (batch: string[]) => T[]
+): T[] {
+  if (ids.length <= SQLITE_BATCH_SIZE) return queryFn(ids);
+  const results: T[] = [];
+  for (let i = 0; i < ids.length; i += SQLITE_BATCH_SIZE) {
+    results.push(...queryFn(ids.slice(i, i + SQLITE_BATCH_SIZE)));
+  }
+  return results;
+}
 
 /**
  * Serialize a number[] embedding to raw float32 bytes for BLOB storage.
@@ -94,6 +116,49 @@ export function hybridRRF(
   return scores;
 }
 
+import type { SearchSignals } from "./memory";
+
+/**
+ * Compute hybrid RRF scores while preserving per-result search signals
+ * (cosine similarity, FTS match, rank positions) for confidence scoring.
+ */
+export function hybridRRFWithSignals(
+  vectorResults: Array<{ id: string; distance: number }>,
+  ftsResults: Array<{ id: string }>,
+  k: number = RRF_K
+): Map<string, SearchSignals & { rrfScore: number }> {
+  const knnMap = new Map<string, { similarity: number; rank: number }>();
+  vectorResults.forEach((r, i) => {
+    knnMap.set(r.id, { similarity: 1 - r.distance, rank: i + 1 });
+  });
+
+  const ftsMap = new Map<string, number>();
+  ftsResults.forEach((r, i) => {
+    ftsMap.set(r.id, i + 1);
+  });
+
+  const allIds = new Set([...knnMap.keys(), ...ftsMap.keys()]);
+  const results = new Map<string, SearchSignals & { rrfScore: number }>();
+
+  for (const id of allIds) {
+    const knn = knnMap.get(id);
+    const ftsRank = ftsMap.get(id) ?? null;
+    let rrfScore = 0;
+    if (knn) rrfScore += 1 / (k + knn.rank);
+    if (ftsRank !== null) rrfScore += 1 / (k + ftsRank);
+
+    results.set(id, {
+      rrfScore,
+      cosineSimilarity: knn?.similarity ?? null,
+      ftsMatch: ftsRank !== null,
+      knnRank: knn?.rank ?? null,
+      ftsRank,
+    });
+  }
+
+  return results;
+}
+
 /**
  * Sort ids by RRF score descending and return top N.
  */

package/server/index.ts

@@ -1,15 +1,15 @@
 #!/usr/bin/env bun
 
-import { loadConfig, parseCliArgs } from "./config/index.js";
-import { connectToDatabase } from "./core/connection.js";
-import { backfillVectors } from "./core/migrations.js";
-import { MemoryRepository } from "./core/memory.repository.js";
-import { ConversationRepository } from "./core/conversation.repository.js";
-import { EmbeddingsService } from "./core/embeddings.service.js";
-import { MemoryService } from "./core/memory.service.js";
-import { ConversationHistoryService } from "./core/conversation.service.js";
-import { startServer } from "./transports/mcp/server.js";
-import { startHttpServer } from "./transports/http/server.js";
+import { loadConfig, parseCliArgs } from "./config/index";
+import { connectToDatabase } from "./core/connection";
+import { backfillVectors } from "./core/migrations";
+import { MemoryRepository } from "./core/memory.repository";
+import { ConversationRepository } from "./core/conversation.repository";
+import { EmbeddingsService } from "./core/embeddings.service";
+import { MemoryService } from "./core/memory.service";
+import { ConversationHistoryService } from "./core/conversation.service";
+import { startServer } from "./transports/mcp/server";
+import { startHttpServer } from "./transports/http/server";
 
 async function main(): Promise<void> {
   const args = process.argv.slice(2);
@@ -25,17 +25,15 @@ async function main(): Promise<void> {
   const overrides = parseCliArgs(args);
   const config = loadConfig(overrides);
 
-  // Initialize database
+  // Initialize database and backfill any missing vectors before services start
   const db = connectToDatabase(config.dbPath);
+  const embeddings = new EmbeddingsService(config.embeddingModel, config.embeddingDimension);
+  await backfillVectors(db, embeddings);
 
   // Initialize layers
   const repository = new MemoryRepository(db);
-  const embeddings = new EmbeddingsService(config.embeddingModel, config.embeddingDimension);
   const memoryService = new MemoryService(repository, embeddings);
 
-  // Backfill any missing vectors (e.g. after vec0-to-BLOB migration)
-  await backfillVectors(db, embeddings);
-
   if (config.pluginMode) {
     console.error("[vector-memory-mcp] Running in plugin mode");
   }

package/server/transports/http/mcp-transport.ts

@@ -21,11 +21,11 @@ import {
 } from "@modelcontextprotocol/sdk/types.js";
 import { InMemoryTransport } from "@modelcontextprotocol/sdk/inMemory.js";
 
-import { tools } from "../mcp/tools.js";
-import { handleToolCall } from "../mcp/handlers.js";
-import { SERVER_INSTRUCTIONS } from "../mcp/server.js";
-import { VERSION } from "../../config/index.js";
-import type { MemoryService } from "../../core/memory.service.js";
+import { tools } from "../mcp/tools";
+import { handleToolCall } from "../mcp/handlers";
+import { SERVER_INSTRUCTIONS } from "../mcp/server";
+import { VERSION } from "../../config/index";
+import type { MemoryService } from "../../core/memory.service";
 
 interface Session {
   server: Server;

package/server/transports/http/server.ts

@@ -3,11 +3,11 @@ import { cors } from "hono/cors";
 import { createServer } from "net";
 import { writeFileSync, mkdirSync, unlinkSync } from "fs";
 import { join } from "path";
-import type { MemoryService } from "../../core/memory.service.js";
-import type { Config } from "../../config/index.js";
-import { isDeleted } from "../../core/memory.js";
-import { createMcpRoutes } from "./mcp-transport.js";
-import type { Memory, SearchIntent } from "../../core/memory.js";
+import type { MemoryService } from "../../core/memory.service";
+import type { Config } from "../../config/index";
+import { isDeleted } from "../../core/memory";
+import { createMcpRoutes } from "./mcp-transport";
+import type { Memory, SearchIntent } from "../../core/memory";
 
 
 /**
@@ -111,10 +111,22 @@ export function createHttpApp(memoryService: MemoryService, config: Config): Hon
         embeddingDimension: config.embeddingDimension,
         historyEnabled: config.conversationHistory.enabled,
         pluginMode: config.pluginMode,
+        embeddingReady: memoryService.getEmbeddings().isReady,
       },
     });
   });
 
+  // Warmup endpoint — triggers ONNX model load if not already cached
+  app.post("/warmup", async (c) => {
+    const embeddings = memoryService.getEmbeddings();
+    if (embeddings.isReady) {
+      return c.json({ status: "already_warm" });
+    }
+    const start = Date.now();
+    await embeddings.warmup();
+    return c.json({ status: "warmed", elapsed: Date.now() - start });
+  });
+
   // Search endpoint
   app.post("/search", async (c) => {
     try {
@@ -127,7 +139,7 @@ export function createHttpApp(memoryService: MemoryService, config: Config): Hon
         return c.json({ error: "Missing or invalid 'query' field" }, 400);
       }
 
-      const results = await memoryService.search(query, intent, limit);
+      const results = await memoryService.search(query, intent, { limit });
 
       return c.json({
         results: results.map((r) => ({
@@ -135,6 +147,7 @@ export function createHttpApp(memoryService: MemoryService, config: Config): Hon
           content: r.content,
           metadata: r.metadata,
           source: r.source,
+          confidence: r.confidence,
           createdAt: r.createdAt.toISOString(),
         })),
         count: results.length,

package/server/transports/mcp/handlers.ts

@@ -1,9 +1,9 @@
 import type { CallToolResult } from "@modelcontextprotocol/sdk/types.js";
-import type { MemoryService } from "../../core/memory.service.js";
-import type { ConversationHistoryService } from "../../core/conversation.service.js";
-import type { SearchIntent } from "../../core/memory.js";
-import type { HistoryFilters, SearchResult } from "../../core/conversation.js";
-import { DEBUG } from "../../config/index.js";
+import type { MemoryService } from "../../core/memory.service";
+import type { ConversationHistoryService } from "../../core/conversation.service";
+import type { SearchIntent } from "../../core/memory";
+import type { HistoryFilters, SearchResult } from "../../core/conversation";
+import { DEBUG } from "../../config/index";
 
 /**
  * Safely coerce a tool argument to an array. Handles the case where the MCP
@@ -51,6 +51,14 @@ function parseDate(value: unknown, fieldName: string): Date | undefined {
   return date;
 }
 
+function requireString(args: Record<string, unknown> | undefined, field: string): string {
+  const value = args?.[field];
+  if (typeof value !== "string" || value.trim() === "") {
+    throw new Error(`${field} is required`);
+  }
+  return value;
+}
+
 export async function handleStoreMemories(
   args: Record<string, unknown> | undefined,
   service: MemoryService
@@ -189,7 +197,9 @@ export async function handleSearchMemories(
     return errorResult(errorText(e));
   }
 
-  const results = await service.search(query, intent, limit, includeDeleted, {
+  const results = await service.search(query, intent, {
+    limit,
+    includeDeleted,
     includeHistory,
     historyOnly,
     historyFilters,
@@ -202,19 +212,7 @@ export async function handleSearchMemories(
     };
   }
 
-  const formatted = results.map((r: SearchResult) => {
-    let result = `[${r.source}] ID: ${r.id}\nContent: ${r.content}`;
-    if (r.metadata && Object.keys(r.metadata).length > 0) {
-      result += `\nMetadata: ${JSON.stringify(r.metadata)}`;
-    }
-    if (r.source === "memory" && includeDeleted && r.supersededBy) {
-      result += `\n[DELETED]`;
-    }
-    if (r.source === "conversation_history" && r.sessionId) {
-      result += `\nSession: ${r.sessionId}`;
-    }
-    return result;
-  });
+  const formatted = results.map((r) => formatSearchResult(r, includeDeleted));
 
   return {
     content: [{ type: "text", text: formatted.join("\n\n---\n\n") }],
@@ -241,6 +239,20 @@ function formatMemoryDetail(
   return result;
 }
 
+function formatSearchResult(r: SearchResult, includeDeleted: boolean): string {
+  let result = `[${r.source}] ID: ${r.id}\nConfidence: ${r.confidence.toFixed(2)}\nContent: ${r.content}`;
+  if (r.metadata && Object.keys(r.metadata).length > 0) {
+    result += `\nMetadata: ${JSON.stringify(r.metadata)}`;
+  }
+  if (r.source === "memory" && includeDeleted && r.supersededBy) {
+    result += `\n[DELETED]`;
+  }
+  if (r.source === "conversation_history" && r.sessionId) {
+    result += `\nSession: ${r.sessionId}`;
+  }
+  return result;
+}
+
 export async function handleGetMemories(
   args: Record<string, unknown> | undefined,
   service: MemoryService
@@ -267,8 +279,11 @@ export async function handleReportMemoryUsefulness(
   args: Record<string, unknown> | undefined,
   service: MemoryService
 ): Promise<CallToolResult> {
-  const memoryId = args?.memory_id as string;
-  const useful = args?.useful as boolean;
+  const memoryId = requireString(args, "memory_id");
+  const useful = args?.useful;
+  if (typeof useful !== "boolean") {
+    return errorResult("useful is required and must be a boolean");
+  }
 
   const memory = await service.vote(memoryId, useful ? 1 : -1);
 
@@ -290,10 +305,19 @@ export async function handleSetWaypoint(
   args: Record<string, unknown> | undefined,
   service: MemoryService
 ): Promise<CallToolResult> {
+  let project: string;
+  let summary: string;
+  try {
+    project = requireString(args, "project");
+    summary = requireString(args, "summary");
+  } catch (e) {
+    return errorResult(errorText(e));
+  }
+
   const memory = await service.setWaypoint({
-    project: args?.project as string,
+    project,
     branch: args?.branch as string | undefined,
-    summary: args?.summary as string,
+    summary,
     completed: (args?.completed as string[] | undefined) ?? [],
     in_progress_blocked: (args?.in_progress_blocked as string[] | undefined) ?? [],
     key_decisions: (args?.key_decisions as string[] | undefined) ?? [],