fix(sqlite): hydrate merged_into_project records on semantic-search ID lookups (closes #3331)

src/services/infrastructure/WorktreeAdoption.ts

@@ -4,7 +4,7 @@ import { existsSync } from 'fs';
 import { spawnSync } from 'child_process';
 import { logger } from '../../utils/logger.js';
 import { getProjectContext } from '../../utils/project-name.js';
-import { ChromaSync } from '../sync/ChromaSync.js';
+import { ChromaSync, MergedIntoProjectTarget } from '../sync/ChromaSync.js';
 import { paths } from '../../shared/paths.js';
 import { openConfiguredSqliteDatabase } from '../sqlite/connection.js';
 
@@ -178,7 +178,7 @@ export async function adoptMergedWorktrees(opts: {
     return result;
   }
 
-  const adoptedSqliteIds: number[] = [];
+  const adoptedChromaTargets: MergedIntoProjectTarget[] = [];
 
   let db: import('bun:sqlite').Database | null = null;
   try {
@@ -207,6 +207,11 @@ export async function adoptMergedWorktrees(opts: {
        WHERE project = ?
          AND (merged_into_project IS NULL OR merged_into_project = ?)`
     );
+    const selectSumForPatch = db.prepare(
+      `SELECT id FROM session_summaries
+       WHERE project = ?
+         AND (merged_into_project IS NULL OR merged_into_project = ?)`
+    );
     const updateObs = db.prepare(
       'UPDATE observations SET merged_into_project = ? WHERE project = ? AND merged_into_project IS NULL'
     );
@@ -220,10 +225,19 @@ export async function adoptMergedWorktrees(opts: {
         worktreeProject,
         parentProject
       ) as Array<{ id: number }>;
+      const summaryRows = selectSumForPatch.all(
+        worktreeProject,
+        parentProject
+      ) as Array<{ id: number }>;
 
       const obsChanges = updateObs.run(parentProject, worktreeProject).changes;
       const sumChanges = updateSum.run(parentProject, worktreeProject).changes;
-      for (const r of rows) adoptedSqliteIds.push(r.id);
+      for (const r of rows) {
+        adoptedChromaTargets.push({ docType: 'observation', sqliteId: r.id });
+      }
+      for (const r of summaryRows) {
+        adoptedChromaTargets.push({ docType: 'session_summary', sqliteId: r.id });
+      }
       result.adoptedObservations += obsChanges;
       result.adoptedSummaries += sumChanges;
     };
@@ -264,27 +278,27 @@ export async function adoptMergedWorktrees(opts: {
     db?.close();
   }
 
-  if (!dryRun && adoptedSqliteIds.length > 0) {
+  if (!dryRun && adoptedChromaTargets.length > 0) {
     const chromaSync = new ChromaSync('claude-mem');
     try {
-      await chromaSync.updateMergedIntoProject(adoptedSqliteIds, parentProject);
-      result.chromaUpdates = adoptedSqliteIds.length;
+      await chromaSync.updateMergedIntoProject(adoptedChromaTargets, parentProject);
+      result.chromaUpdates = adoptedChromaTargets.length;
     } catch (err) {
       if (err instanceof Error) {
         logger.error(
           'SYSTEM',
           'Worktree adoption Chroma patch failed (SQL already committed)',
-          { parentProject, sqliteIdCount: adoptedSqliteIds.length },
+          { parentProject, sqliteIdCount: adoptedChromaTargets.length },
           err
         );
       } else {
         logger.error(
           'SYSTEM',
           'Worktree adoption Chroma patch failed (SQL already committed)',
-          { parentProject, sqliteIdCount: adoptedSqliteIds.length, error: String(err) }
+          { parentProject, sqliteIdCount: adoptedChromaTargets.length, error: String(err) }
         );
       }
-      result.chromaFailed = adoptedSqliteIds.length;
+      result.chromaFailed = adoptedChromaTargets.length;
     }
   }
 

src/services/sqlite/SessionStore.ts

@@ -1744,8 +1744,8 @@ export class SessionStore {
     const additionalConditions: string[] = [];
 
     if (project) {
-      additionalConditions.push('o.project = ?');
-      params.push(project);
+      additionalConditions.push('(o.project = ? OR o.merged_into_project = ?)');
+      params.push(project, project);
     }
 
     if (platformSource) {
@@ -2190,8 +2190,8 @@ export class SessionStore {
     const additionalConditions: string[] = [];
 
     if (project) {
-      additionalConditions.push('ss.project = ?');
-      params.push(project);
+      additionalConditions.push('(ss.project = ? OR ss.merged_into_project = ?)');
+      params.push(project, project);
     }
 
     if (platformSource) {
@@ -2295,13 +2295,18 @@ export class SessionStore {
     prompts: any[];
   } {
     const normalizedPlatformSource = platformSource ? normalizePlatformSource(platformSource) : undefined;
-    const buildScope = (rowAlias: string, sessionAlias: string): { clause: string; params: any[] } => {
+    const buildScope = (rowAlias: string, sessionAlias: string, includeMergedProject: boolean = false): { clause: string; params: any[] } => {
       const conditions: string[] = [];
       const params: any[] = [];
 
       if (project) {
-        conditions.push(`${rowAlias}.project = ?`);
-        params.push(project);
+        if (includeMergedProject) {
+          conditions.push(`(${rowAlias}.project = ? OR ${rowAlias}.merged_into_project = ?)`);
+          params.push(project, project);
+        } else {
+          conditions.push(`${rowAlias}.project = ?`);
+          params.push(project);
+        }
       }
 
       if (normalizedPlatformSource) {
@@ -2314,8 +2319,8 @@ export class SessionStore {
         params
       };
     };
-    const observationScope = buildScope('o', 'src');
-    const summaryScope = buildScope('ss', 'src');
+    const observationScope = buildScope('o', 'src', true);
+    const summaryScope = buildScope('ss', 'src', true);
     const promptScope = buildScope('s', 's');
 
     let startEpoch: number;

src/services/sync/ChromaSync.ts

@@ -44,6 +44,11 @@ export interface ChromaDocument {
   metadata: Record<string, string | number>;
 }
 
+export interface MergedIntoProjectTarget {
+  docType: 'observation' | 'session_summary';
+  sqliteId: number;
+}
+
 interface StoredObservation {
   id: number;
   memory_session_id: string;
@@ -986,52 +991,63 @@ export class ChromaSync {
   }
 
   async updateMergedIntoProject(
-    sqliteIds: number[],
+    targets: MergedIntoProjectTarget[],
     mergedIntoProject: string
   ): Promise<void> {
-    if (sqliteIds.length === 0) return;
+    if (targets.length === 0) return;
 
     await this.ensureCollectionExists();
     const chromaMcp = ChromaMcpManager.getInstance();
 
     let totalPatched = 0;
 
-    for (let i = 0; i < sqliteIds.length; i += this.BATCH_SIZE) {
-      const idBatch = sqliteIds.slice(i, i + this.BATCH_SIZE);
+    for (const docType of ['observation', 'session_summary'] as const) {
+      const sqliteIds = targets
+        .filter(target => target.docType === docType)
+        .map(target => target.sqliteId);
 
-      const existing = await chromaMcp.callTool('chroma_get_documents', {
-        collection_name: this.collectionName,
-        where: { sqlite_id: { $in: idBatch } },
-        include: ['metadatas']
-      }) as { ids?: string[]; metadatas?: Array<Record<string, any> | null> };
-
-      const docIds: string[] = existing?.ids ?? [];
-      if (docIds.length === 0) continue;
-
-      const metadatas = (existing?.metadatas ?? []).map(m => {
-        const merged: Record<string, any> = {
-          ...(m ?? {}),
-          merged_into_project: mergedIntoProject
-        };
-        return Object.fromEntries(
-          Object.entries(merged).filter(
-            ([, v]) => v !== null && v !== undefined && v !== ''
-          )
-        );
-      });
+      for (let i = 0; i < sqliteIds.length; i += this.BATCH_SIZE) {
+        const idBatch = sqliteIds.slice(i, i + this.BATCH_SIZE);
 
-      await chromaMcp.callTool('chroma_update_documents', {
-        collection_name: this.collectionName,
-        ids: docIds,
-        metadatas
-      });
-      totalPatched += docIds.length;
+        const existing = await chromaMcp.callTool('chroma_get_documents', {
+          collection_name: this.collectionName,
+          where: {
+            $and: [
+              { doc_type: docType },
+              { sqlite_id: { $in: idBatch } }
+            ]
+          },
+          include: ['metadatas']
+        }) as { ids?: string[]; metadatas?: Array<Record<string, any> | null> };
+
+        const docIds: string[] = existing?.ids ?? [];
+        if (docIds.length === 0) continue;
+
+        const metadatas = (existing?.metadatas ?? []).map(m => {
+          const merged: Record<string, any> = {
+            ...(m ?? {}),
+            merged_into_project: mergedIntoProject
+          };
+          return Object.fromEntries(
+            Object.entries(merged).filter(
+              ([, v]) => v !== null && v !== undefined && v !== ''
+            )
+          );
+        });
+
+        await chromaMcp.callTool('chroma_update_documents', {
+          collection_name: this.collectionName,
+          ids: docIds,
+          metadatas
+        });
+        totalPatched += docIds.length;
+      }
     }
 
     logger.info('CHROMA_SYNC', 'merged_into_project metadata patched', {
       collection: this.collectionName,
       mergedIntoProject,
-      sqliteIdCount: sqliteIds.length,
+      sqliteIdCount: targets.length,
       chromaDocsPatched: totalPatched
     });
   }

tests/context/formatters/agent-formatter.test.ts

@@ -1,4 +1,8 @@
-import { describe, it, expect, mock, beforeEach } from 'bun:test';
+import { describe, it, expect, mock, beforeEach, afterAll } from 'bun:test';
+
+import * as realModeManager from '../../../src/services/domain/ModeManager.js';
+
+const realModeManagerSnapshot = { ...realModeManager };
 
 mock.module('../../../src/services/domain/ModeManager.js', () => ({
   ModeManager: {
@@ -90,6 +94,10 @@ function createTestConfig(overrides: Partial<ContextConfig> = {}): ContextConfig
   };
 }
 
+afterAll(() => {
+  mock.module('../../../src/services/domain/ModeManager.js', () => realModeManagerSnapshot);
+});
+
 describe('AgentFormatter', () => {
   describe('renderAgentHeader', () => {
     it('should produce valid markdown header with project name', () => {

tests/hooks/server-client.test.ts

@@ -1,6 +1,10 @@
 // SPDX-License-Identifier: Apache-2.0
 
-import { describe, it, expect, beforeEach, afterEach, mock } from 'bun:test';
+import { describe, it, expect, beforeEach, afterEach, afterAll, mock } from 'bun:test';
+
+import * as realWorkerUtils from '../../src/shared/worker-utils.js';
+
+const realWorkerUtilsSnapshot = { ...realWorkerUtils };
 
 mock.module('../../src/shared/worker-utils.js', () => ({
   fetchWithTimeout: async (url: string, init: RequestInit, _timeoutMs: number) => {
@@ -53,6 +57,10 @@ describe('ServerClient', () => {
     globalThis.fetch = originalFetch;
   });
 
+  afterAll(() => {
+    mock.module('../../src/shared/worker-utils.js', () => realWorkerUtilsSnapshot);
+  });
+
   it('throws missing_api_key when apiKey is empty', async () => {
     const client = new ServerClient({ serverBaseUrl: 'http://x', apiKey: '' });
     let caught: unknown;