feat(worktree): adoption engine for merged worktrees

Detects merged worktrees via git (worktree list --porcelain +
branch --merged HEAD), then stamps merged_into_project on SQLite
observations/summaries and propagates the same metadata to Chroma
in lockstep. `project` stays immutable; adoption is a virtual
pointer. Idempotent via IS NULL guard on UPDATE and by idempotent
Chroma metadata writes. SQL is source of truth — Chroma failures
are logged but don't roll back SQL.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

src/services/infrastructure/WorktreeAdoption.ts

@@ -0,0 +1,281 @@
+/**
+ * WorktreeAdoption - Stamp observations from merged worktrees into their parent project.
+ *
+ * Given a parent repo path, this engine:
+ *   1. Uses git to enumerate worktrees of the parent repo.
+ *   2. Classifies each worktree's branch as "merged" (in `git branch --merged HEAD`)
+ *      or manually overridden via `onlyBranch` (for squash-merge detection).
+ *   3. Stamps `merged_into_project` on `observations` and `session_summaries` rows
+ *      whose `project` matches the composite `parent/worktree` name.
+ *   4. Propagates the same metadata to Chroma so semantic search includes the
+ *      adopted rows under the parent project.
+ *
+ * `project` is never overwritten — it remains immutable provenance. The
+ * `merged_into_project` column is a virtual pointer that query layers OR into
+ * their WHERE predicates.
+ *
+ * DB lifecycle mirrors `runOneTimeCwdRemap` in ProcessManager.ts: we manage our
+ * own Database handle (open -> transaction -> close in finally) so this engine
+ * can be called on worker startup before `dbManager.initialize()` without
+ * contending on the shared handle.
+ */
+
+import path from 'path';
+import { homedir } from 'os';
+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';
+
+const DEFAULT_DATA_DIR = path.join(homedir(), '.claude-mem');
+
+export interface AdoptionResult {
+  repoPath: string;
+  parentProject: string;
+  scannedWorktrees: number;
+  mergedBranches: string[];
+  adoptedObservations: number;
+  adoptedSummaries: number;
+  chromaUpdates: number;
+  chromaFailed: number;
+  dryRun: boolean;
+  errors: Array<{ worktree: string; error: string }>;
+}
+
+interface WorktreeEntry {
+  path: string;
+  branch: string | null;
+}
+
+function gitCapture(cwd: string, args: string[]): string | null {
+  const r = spawnSync('git', ['-C', cwd, ...args], { encoding: 'utf8' });
+  if (r.status !== 0) return null;
+  return (r.stdout ?? '').trim();
+}
+
+/**
+ * Resolve the main working-tree root for an arbitrary cwd inside a repo or worktree.
+ * Mirrors the handling in `scripts/cwd-remap.ts:48-51`.
+ */
+function resolveMainRepoPath(cwd: string): string | null {
+  const commonDir = gitCapture(cwd, [
+    'rev-parse',
+    '--path-format=absolute',
+    '--git-common-dir'
+  ]);
+  if (!commonDir) return null;
+
+  // Normal: common-dir is "<repo>/.git". Bare: strip the trailing ".git".
+  const mainRoot = commonDir.endsWith('/.git')
+    ? path.dirname(commonDir)
+    : commonDir.replace(/\.git$/, '');
+  return existsSync(mainRoot) ? mainRoot : null;
+}
+
+function listWorktrees(mainRepo: string): WorktreeEntry[] {
+  const raw = gitCapture(mainRepo, ['worktree', 'list', '--porcelain']);
+  if (!raw) return [];
+
+  const entries: WorktreeEntry[] = [];
+  let current: Partial<WorktreeEntry> = {};
+  for (const line of raw.split('\n')) {
+    if (line.startsWith('worktree ')) {
+      if (current.path) entries.push({ path: current.path, branch: current.branch ?? null });
+      current = { path: line.slice('worktree '.length).trim(), branch: null };
+    } else if (line.startsWith('branch ')) {
+      // `branch refs/heads/<name>` — strip the ref prefix.
+      const refName = line.slice('branch '.length).trim();
+      current.branch = refName.startsWith('refs/heads/')
+        ? refName.slice('refs/heads/'.length)
+        : refName;
+    } else if (line === '' && current.path) {
+      entries.push({ path: current.path, branch: current.branch ?? null });
+      current = {};
+    }
+  }
+  if (current.path) entries.push({ path: current.path, branch: current.branch ?? null });
+  return entries;
+}
+
+function listMergedBranches(mainRepo: string): Set<string> {
+  const raw = gitCapture(mainRepo, [
+    'branch',
+    '--merged',
+    'HEAD',
+    '--format=%(refname:short)'
+  ]);
+  if (!raw) return new Set();
+  return new Set(
+    raw.split('\n').map(b => b.trim()).filter(b => b.length > 0)
+  );
+}
+
+/**
+ * Stamp `merged_into_project` on observations and session_summaries for every
+ * worktree of `opts.repoPath` whose branch has been merged into the parent's HEAD.
+ *
+ * Idempotent: a row is only touched when its `merged_into_project IS NULL`.
+ *
+ * Chroma is patched AFTER SQL commits. Chroma failure does NOT roll back SQL —
+ * SQL is source of truth; a subsequent run will retry the Chroma patch because
+ * the filter in `updateMergedIntoProject` keys on `sqlite_id`.
+ */
+export async function adoptMergedWorktrees(opts: {
+  repoPath?: string;
+  dataDirectory?: string;
+  dryRun?: boolean;
+  onlyBranch?: string;
+} = {}): Promise<AdoptionResult> {
+  const dataDirectory = opts.dataDirectory ?? DEFAULT_DATA_DIR;
+  const dryRun = opts.dryRun ?? false;
+  const startCwd = opts.repoPath ?? process.cwd();
+
+  const mainRepo = resolveMainRepoPath(startCwd);
+  const parentProject = mainRepo ? getProjectContext(mainRepo).primary : '';
+
+  const result: AdoptionResult = {
+    repoPath: mainRepo ?? startCwd,
+    parentProject,
+    scannedWorktrees: 0,
+    mergedBranches: [],
+    adoptedObservations: 0,
+    adoptedSummaries: 0,
+    chromaUpdates: 0,
+    chromaFailed: 0,
+    dryRun,
+    errors: []
+  };
+
+  if (!mainRepo) {
+    logger.debug('SYSTEM', 'Worktree adoption skipped (not a git repo)', { startCwd });
+    return result;
+  }
+
+  const dbPath = path.join(dataDirectory, 'claude-mem.db');
+  if (!existsSync(dbPath)) {
+    logger.debug('SYSTEM', 'Worktree adoption skipped (no DB yet)', { dbPath });
+    return result;
+  }
+
+  const allWorktrees = listWorktrees(mainRepo);
+  const childWorktrees = allWorktrees.filter(w => w.path !== mainRepo);
+  result.scannedWorktrees = childWorktrees.length;
+
+  if (childWorktrees.length === 0) {
+    return result;
+  }
+
+  let targets: WorktreeEntry[];
+  if (opts.onlyBranch) {
+    targets = childWorktrees.filter(w => w.branch === opts.onlyBranch);
+  } else {
+    const merged = listMergedBranches(mainRepo);
+    targets = childWorktrees.filter(w => w.branch !== null && merged.has(w.branch));
+  }
+
+  result.mergedBranches = targets
+    .map(t => t.branch)
+    .filter((b): b is string => b !== null);
+
+  if (targets.length === 0) {
+    return result;
+  }
+
+  const adoptedSqliteIds: number[] = [];
+
+  let db: import('bun:sqlite').Database | null = null;
+  try {
+    const { Database } = require('bun:sqlite') as typeof import('bun:sqlite');
+    db = new Database(dbPath);
+
+    const selectObs = db.prepare(
+      'SELECT id FROM observations WHERE project = ? AND merged_into_project IS NULL'
+    );
+    const updateObs = db.prepare(
+      'UPDATE observations SET merged_into_project = ? WHERE project = ? AND merged_into_project IS NULL'
+    );
+    const updateSum = db.prepare(
+      'UPDATE session_summaries SET merged_into_project = ? WHERE project = ? AND merged_into_project IS NULL'
+    );
+
+    const tx = db.transaction(() => {
+      for (const wt of targets) {
+        try {
+          const worktreeProject = getProjectContext(wt.path).primary;
+          const rows = selectObs.all(worktreeProject) as Array<{ id: number }>;
+          for (const r of rows) adoptedSqliteIds.push(r.id);
+
+          const obsChanges = updateObs.run(parentProject, worktreeProject).changes;
+          const sumChanges = updateSum.run(parentProject, worktreeProject).changes;
+          result.adoptedObservations += obsChanges;
+          result.adoptedSummaries += sumChanges;
+        } catch (err) {
+          const message = err instanceof Error ? err.message : String(err);
+          logger.warn('SYSTEM', 'Worktree adoption skipped branch', {
+            worktree: wt.path,
+            branch: wt.branch,
+            error: message
+          });
+          result.errors.push({ worktree: wt.path, error: message });
+        }
+      }
+      if (dryRun) {
+        // Throw to force rollback. Sentinel caught below.
+        throw new Error('__DRY_RUN_ROLLBACK__');
+      }
+    });
+
+    try {
+      tx();
+    } catch (err) {
+      const message = err instanceof Error ? err.message : String(err);
+      if (message === '__DRY_RUN_ROLLBACK__') {
+        // Rolled back as intended for dry-run — counts are still useful.
+      } else {
+        throw err;
+      }
+    }
+  } finally {
+    db?.close();
+  }
+
+  if (!dryRun && adoptedSqliteIds.length > 0) {
+    const chromaSync = new ChromaSync('claude-mem');
+    try {
+      await chromaSync.updateMergedIntoProject(adoptedSqliteIds, parentProject);
+      result.chromaUpdates = adoptedSqliteIds.length;
+    } catch (err) {
+      logger.error(
+        'CHROMA_SYNC',
+        'Worktree adoption Chroma patch failed (SQL already committed)',
+        { parentProject, sqliteIdCount: adoptedSqliteIds.length },
+        err as Error
+      );
+      result.chromaFailed = adoptedSqliteIds.length;
+    } finally {
+      await chromaSync.close();
+    }
+  }
+
+  if (
+    result.adoptedObservations > 0 ||
+    result.adoptedSummaries > 0 ||
+    result.chromaUpdates > 0 ||
+    result.errors.length > 0
+  ) {
+    logger.info('SYSTEM', 'Worktree adoption applied', {
+      parentProject,
+      dryRun,
+      scannedWorktrees: result.scannedWorktrees,
+      mergedBranches: result.mergedBranches,
+      adoptedObservations: result.adoptedObservations,
+      adoptedSummaries: result.adoptedSummaries,
+      chromaUpdates: result.chromaUpdates,
+      chromaFailed: result.chromaFailed,
+      errors: result.errors.length
+    });
+  }
+
+  return result;
+}

src/services/sync/ChromaSync.ts

@@ -830,6 +830,72 @@ export class ChromaSync {
     }
   }
 
+  /**
+   * Stamp `merged_into_project` on every Chroma document whose metadata
+   * `sqlite_id` is in the provided set. Used by the worktree adoption engine
+   * to keep Chroma's metadata in lockstep with SQLite after a parent branch
+   * absorbs a worktree branch via merge.
+   *
+   * Batched: fetches docs by `sqlite_id IN sqliteIds`, rewrites metadata with
+   * the new field, and calls `chroma_update_documents` once per page of up to
+   * BATCH_SIZE ids. Idempotent — re-running with the same value is a no-op
+   * because the write doesn't depend on the prior value.
+   */
+  async updateMergedIntoProject(
+    sqliteIds: number[],
+    mergedIntoProject: string
+  ): Promise<void> {
+    if (sqliteIds.length === 0) return;
+
+    await this.ensureCollectionExists();
+    const chromaMcp = ChromaMcpManager.getInstance();
+
+    let totalPatched = 0;
+
+    // Chunk the sqlite_id set to keep each Chroma call bounded.
+    for (let i = 0; i < sqliteIds.length; i += this.BATCH_SIZE) {
+      const idBatch = sqliteIds.slice(i, i + this.BATCH_SIZE);
+
+      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 => {
+        // Merge old metadata with the new field, then filter out null/undefined/''
+        // to match the sanitization other callTool sites apply (chroma-mcp
+        // rejects null values in metadata).
+        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,
+      chromaDocsPatched: totalPatched
+    });
+  }
+
   /**
    * Close the ChromaSync instance
    * ChromaMcpManager is a singleton and manages its own lifecycle