Fix 20 bugs from full codebase review

src/config/loader.ts

@@ -264,12 +264,24 @@ function applyEnvMappings(config: ExternalConfig, mappings: EnvMapping[]): void
 
     const key = parts[parts.length - 1];
     switch (type) {
-      case 'int':
-        obj[key] = parseInt(value, 10);
+      case 'int': {
+        const parsed = parseInt(value, 10);
+        if (isNaN(parsed)) {
+          log.warn(`Invalid integer for ${env}: '${value}'`);
+          continue;
+        }
+        obj[key] = parsed;
         break;
-      case 'float':
-        obj[key] = parseFloat(value);
+      }
+      case 'float': {
+        const parsed = parseFloat(value);
+        if (isNaN(parsed)) {
+          log.warn(`Invalid float for ${env}: '${value}'`);
+          continue;
+        }
+        obj[key] = parsed;
         break;
+      }
       case 'boolean':
         obj[key] = value === 'true';
         break;
@@ -381,6 +393,25 @@ export function validateExternalConfig(config: ExternalConfig): string[] {
     }
   }
 
+  // Maintenance validation
+  if (config.maintenance?.clusterHour !== undefined) {
+    if (config.maintenance.clusterHour < 0 || config.maintenance.clusterHour > 23) {
+      errors.push('maintenance.clusterHour must be between 0 and 23 (inclusive)');
+    }
+  }
+
+  // Recency validation
+  if (config.recency?.halfLifeHours !== undefined) {
+    if (config.recency.halfLifeHours <= 0) {
+      errors.push('recency.halfLifeHours must be greater than 0');
+    }
+  }
+  if (config.recency?.decayFactor !== undefined) {
+    if (config.recency.decayFactor < 0) {
+      errors.push('recency.decayFactor must be >= 0');
+    }
+  }
+
   // Length penalty validation
   if (config.lengthPenalty?.referenceTokens !== undefined) {
     if (config.lengthPenalty.referenceTokens <= 0) {

src/config/memory-config.ts

@@ -225,11 +225,45 @@ export const DEFAULT_CONFIG: MemoryConfig = {
   },
 };
 
+/**
+ * Cached runtime config, populated by initRuntimeConfig().
+ * When set, getConfig() returns this instead of bare defaults,
+ * ensuring user config files and env vars are respected.
+ */
+let _runtimeConfig: MemoryConfig | null = null;
+
+/**
+ * Initialize the runtime config cache. Call once at startup (e.g., MCP server start).
+ * This ensures getConfig() respects user config files and env vars.
+ */
+export function initRuntimeConfig(config: MemoryConfig): void {
+  _runtimeConfig = config;
+}
+
 /**
  * Get configuration with overrides applied.
+ * Returns the cached runtime config (from initRuntimeConfig) if available,
+ * otherwise falls back to DEFAULT_CONFIG.
  */
 export function getConfig(overrides: Partial<MemoryConfig> = {}): MemoryConfig {
-  return { ...DEFAULT_CONFIG, ...overrides };
+  const base = _runtimeConfig ?? DEFAULT_CONFIG;
+  if (Object.keys(overrides).length === 0) return base;
+  return {
+    ...base,
+    ...overrides,
+    // Deep-merge nested objects to prevent shallow spread from destroying them
+    hybridSearch: { ...base.hybridSearch, ...overrides.hybridSearch },
+    clusterExpansion: { ...base.clusterExpansion, ...overrides.clusterExpansion },
+    mmrReranking: { ...base.mmrReranking, ...overrides.mmrReranking },
+    recency: { ...base.recency, ...overrides.recency },
+    lengthPenalty: { ...base.lengthPenalty, ...overrides.lengthPenalty },
+    repomap: {
+      ...base.repomap,
+      ...overrides.repomap,
+      languages: overrides.repomap?.languages ?? base.repomap.languages,
+    },
+    semanticIndex: { ...base.semanticIndex, ...overrides.semanticIndex },
+  };
 }
 
 /**

src/dashboard/server.ts

@@ -58,7 +58,11 @@ export function createApp() {
 }
 
 export async function startDashboard(port: number): Promise<void> {
-  // Ensure database is initialized before starting
+  // Ensure config and database are initialized before starting
+  const { initRuntimeConfig } = await import('../config/memory-config.js');
+  const { loadConfig, toRuntimeConfig } = await import('../config/loader.js');
+  initRuntimeConfig(toRuntimeConfig(loadConfig()));
+
   const { getDb } = await import('../storage/db.js');
   getDb();
 

src/hooks/hook-utils.ts

@@ -116,6 +116,7 @@ export async function withRetry<T>(
   hookName: string,
   fn: () => Promise<T>,
   options: RetryOptions = {},
+  metrics?: HookMetrics,
 ): Promise<T> {
   const {
     maxRetries = 3,
@@ -130,6 +131,7 @@ export async function withRetry<T>(
   for (let attempt = 0; attempt <= maxRetries; attempt++) {
     try {
       if (attempt > 0) {
+        if (metrics) metrics.retryCount = attempt;
         const delay = calculateBackoff(attempt - 1, initialDelayMs, maxDelayMs, backoffFactor);
 
         logHook({
@@ -229,7 +231,7 @@ export async function executeHook<T>(
     let result: T;
 
     if (options.retry) {
-      result = await withRetry(hookName, fn, options.retry);
+      result = await withRetry(hookName, fn, options.retry, metrics);
     } else {
       result = await fn();
     }

src/hooks/session-start.ts

@@ -20,7 +20,8 @@ import {
   getSessionsForProject,
   getChunksByTimeRange,
 } from '../storage/chunk-store.js';
-import { getConfig } from '../config/memory-config.js';
+import { getConfig, initRuntimeConfig } from '../config/memory-config.js';
+import { loadConfig, toRuntimeConfig } from '../config/loader.js';
 import { approximateTokens } from '../utils/token-counter.js';
 import { runStaleMaintenanceTasks } from '../maintenance/scheduler.js';
 import { executeHook, logHook, isTransientError, type HookMetrics } from './hook-utils.js';
@@ -193,6 +194,9 @@ export async function handleSessionStart(
 ): Promise<SessionStartResult> {
   const { enableRetry = true, maxRetries = 3, gracefulDegradation = true } = options;
 
+  // Ensure user config is loaded before getConfig() is used
+  initRuntimeConfig(toRuntimeConfig(loadConfig()));
+
   // Run stale maintenance tasks in background (prune, recluster)
   // Covers cases where scheduled cron times were missed (e.g. laptop asleep)
   runStaleMaintenanceTasks();
@@ -217,7 +221,7 @@ export async function handleSessionStart(
               retryOn: isTransientError,
             }
           : undefined,
-        fallback: gracefulDegradation ? undefined : undefined,
+        fallback: gracefulDegradation ? fallbackResult : undefined,
         project: basename(projectPath) || projectPath,
       },
     );

src/ingest/brief-debrief-detector.ts

@@ -234,13 +234,14 @@ export function detectDebriefPoints(
         const turn = mainTurns[i];
         if (extractSpawnedAgentIds(turn).includes(agentId)) {
           // Link to the next turn's chunks (all of them)
-          const nextChunkIds = chunkIdsByTurn.get(i + 1);
+          const nextTurnIndex = i + 1 < mainTurns.length ? mainTurns[i + 1].index : -1;
+          const nextChunkIds = nextTurnIndex >= 0 ? chunkIdsByTurn.get(nextTurnIndex) : undefined;
           if (nextChunkIds && nextChunkIds.length > 0) {
             debriefPoints.push({
               agentId,
               agentFinalChunkIds: finalChunkIds,
               parentChunkIds: [...nextChunkIds],
-              turnIndex: i + 1,
+              turnIndex: nextTurnIndex,
               spawnDepth,
             });
           }
@@ -281,7 +282,7 @@ function findDebriefTurn(turns: Turn[], agentId: string, _finalChunk: Chunk): nu
         // Only match if the result explicitly contains this agent's ID
         // (removed isTaskResult fallback - it's too broad and matches unrelated agents)
         if (exchange.result.includes(agentId)) {
-          return i;
+          return turn.index;
         }
       }
     }
@@ -291,7 +292,7 @@ function findDebriefTurn(turns: Turn[], agentId: string, _finalChunk: Chunk): nu
       if (msg.type === 'user' && msg.message?.content) {
         const content = msg.message.content;
         if (typeof content === 'string' && content.includes(agentId)) {
-          return i;
+          return turn.index;
         }
       }
     }
@@ -303,7 +304,7 @@ function findDebriefTurn(turns: Turn[], agentId: string, _finalChunk: Chunk): nu
     if (extractSpawnedAgentIds(turn).includes(agentId)) {
       // Return the next turn if it exists
       if (i + 1 < turns.length) {
-        return i + 1;
+        return turns[i + 1].index;
       }
     }
   }

src/mcp/server.ts

@@ -13,6 +13,8 @@
 import { createInterface } from 'readline';
 import { tools, getTool } from './tools.js';
 import { getDb, closeDb } from '../storage/db.js';
+import { initRuntimeConfig } from '../config/memory-config.js';
+import { loadConfig, toRuntimeConfig } from '../config/loader.js';
 import { disposeRetrieval } from '../retrieval/context-assembler.js';
 import { getChunkCount } from '../storage/chunk-store.js';
 import { getEdgeCount } from '../storage/edge-store.js';
@@ -82,7 +84,7 @@ interface McpRequest {
  */
 interface McpResponse {
   jsonrpc: '2.0';
-  id: string | number;
+  id: string | number | null;
   result?: unknown;
   error?: {
     code: number;
@@ -113,7 +115,7 @@ interface HealthStatus {
  * Create a standardized error response.
  */
 function createErrorResponse(
-  id: string | number,
+  id: string | number | null,
   code: number,
   message: string,
   data?: unknown,
@@ -176,7 +178,8 @@ export class McpServer {
     this.running = true;
     this.startTime = Date.now();
 
-    // Initialize database
+    // Initialize config and database
+    initRuntimeConfig(toRuntimeConfig(loadConfig()));
     getDb();
 
     this.log({ level: 'info', event: 'server_started' });
@@ -229,7 +232,7 @@ export class McpServer {
       } catch (error) {
         this.errorCount++;
         const errorResponse = createErrorResponse(
-          0,
+          null,
           ErrorCodes.PARSE_ERROR,
           'Parse error',
           errorMessage(error),
@@ -326,11 +329,22 @@ export class McpServer {
         case 'tools/list':
           return this.handleToolsList(id);
 
-        case 'tools/call':
-          return await this.handleToolsCall(
-            id,
-            params as { name: string; arguments: Record<string, unknown> },
-          );
+        case 'tools/call': {
+          const toolParams = params as
+            | { name: string; arguments?: Record<string, unknown> }
+            | undefined;
+          if (!toolParams || typeof toolParams.name !== 'string') {
+            return createErrorResponse(
+              id,
+              ErrorCodes.INVALID_PARAMS,
+              'tools/call requires params.name',
+            );
+          }
+          return await this.handleToolsCall(id, {
+            name: toolParams.name,
+            arguments: toolParams.arguments ?? {},
+          });
+        }
 
         case 'ping':
           return this.handlePing(id);

src/mcp/tools.ts

@@ -351,7 +351,7 @@ export const listSessionsTool: ToolDefinition = {
     const daysBack = args.days_back as number | undefined;
     const limit = (args.limit as number | undefined) ?? 30;
 
-    if (daysBack !== null && daysBack !== undefined) {
+    if (daysBack !== undefined && daysBack > 0 && from === undefined && to === undefined) {
       to = new Date().toISOString();
       from = new Date(Date.now() - daysBack * 24 * 60 * 60 * 1000).toISOString();
     }

src/models/embedder.ts

@@ -99,6 +99,8 @@ export class Embedder {
         throw epError;
       }
     }
+
+    // Only set config after pipeline is successfully loaded
     this.config = config;
 
     const loadTimeMs = performance.now() - start;

src/retrieval/chain-walker.ts

@@ -180,8 +180,9 @@ async function walkAllPaths(
       if (agentFilter && chunk.agentId !== agentFilter) {
         const newSkips = consecutiveSkips + 1;
         if (newSkips <= maxSkippedConsecutive) {
+          const before = candidates.length;
           await dfs(nextId, depth + 1, newSkips);
-          anyChildEmitted = true;
+          if (candidates.length > before) anyChildEmitted = true;
         }
         pathVisited.delete(nextId);
         continue;
@@ -193,8 +194,9 @@ async function walkAllPaths(
       // adding to path. The chain doesn't break — we continue traversing — but
       // this node won't appear in the output or affect the median score.
       if (chunkTokens > tokenBudget) {
+        const before = candidates.length;
         await dfs(nextId, depth + 1, 0);
-        anyChildEmitted = true;
+        if (candidates.length > before) anyChildEmitted = true;
         pathVisited.delete(nextId);
         continue;
       }

src/storage/chunk-store.ts

@@ -211,6 +211,7 @@ export function isSessionIngested(sessionId: string): boolean {
 export function deleteChunk(id: string): boolean {
   const db = getDb();
   const result = db.prepare('DELETE FROM chunks WHERE id = ?').run(id);
+  invalidateProjectsCache();
   return result.changes > 0;
 }
 
@@ -225,6 +226,7 @@ export function deleteChunks(ids: string[]): number {
   const db = getDb();
   const placeholders = sqlPlaceholders(ids.length);
   const result = db.prepare(`DELETE FROM chunks WHERE id IN (${placeholders})`).run(...ids);
+  invalidateProjectsCache();
   return result.changes;
 }