fix(worktree): address PR review — schema guard, startup adoption, query parity

Addresses six CodeRabbit/Greptile findings on PR #2052:

- Schema guard in adoptMergedWorktrees probes for merged_into_project
  columns before preparing statements; returns early when absent so first
  boot after upgrade (pre-migration) doesn't silently fail.

- Startup adoption now iterates distinct cwds from pending_messages and
  dedupes via resolveMainRepoPath — the worker daemon runs with
  cwd=plugin scripts dir, so process.cwd() fallback was a no-op.

- ObservationCompiler single-project queries (queryObservations /
  querySummaries) OR merged_into_project into WHERE so injected context
  surfaces adopted worktree rows, matching the Multi variants.

- SessionStore constructor now calls ensureMergedIntoProjectColumns so
  bundled artifacts (context-generator.cjs) that embed SessionStore get
  the merged_into_project column on DBs that only went through the
  bundled migration chain.

- OBSERVER_SESSIONS_PROJECT constant is now derived from
  basename(OBSERVER_SESSIONS_DIR) and used across PaginationHelper,
  SessionStore, and timeline queries instead of hardcoded strings.

- Corrected misleading Chroma retry docstring in WorktreeAdoption to
  match actual behavior (no auto-retry once SQL commits).

src/services/context/ObservationCompiler.ts

@@ -52,7 +52,7 @@ export function queryObservations(
       o.created_at_epoch
     FROM observations o
     LEFT JOIN sdk_sessions s ON o.memory_session_id = s.memory_session_id
-    WHERE o.project = ?
+    WHERE (o.project = ? OR o.merged_into_project = ?)
       AND type IN (${typePlaceholders})
       AND EXISTS (
         SELECT 1 FROM json_each(o.concepts)
@@ -62,6 +62,7 @@ export function queryObservations(
     ORDER BY o.created_at_epoch DESC
     LIMIT ?
   `).all(
+    project,
     project,
     ...typeArray,
     ...conceptArray,
@@ -93,12 +94,12 @@ export function querySummaries(
       ss.created_at_epoch
     FROM session_summaries ss
     LEFT JOIN sdk_sessions s ON ss.memory_session_id = s.memory_session_id
-    WHERE ss.project = ?
+    WHERE (ss.project = ? OR ss.merged_into_project = ?)
       ${platformSource ? "AND COALESCE(s.platform_source, 'claude') = ?" : ''}
     ORDER BY ss.created_at_epoch DESC
     LIMIT ?
   `).all(
-    ...[project, ...(platformSource ? [platformSource] : []), config.sessionCount + SUMMARY_LOOKAHEAD]
+    ...[project, project, ...(platformSource ? [platformSource] : []), config.sessionCount + SUMMARY_LOOKAHEAD]
   ) as SessionSummary[];
 }
 

src/services/infrastructure/WorktreeAdoption.ts

@@ -130,8 +130,12 @@ function listMergedBranches(mainRepo: string): Set<string> {
  * 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`.
+ * SQL is source of truth. A transient Chroma failure does NOT auto-retry:
+ * once SQL commits, `merged_into_project IS NULL` no longer matches those rows,
+ * so the same adoption pass won't rediscover them. If Chroma patching fails,
+ * `result.chromaFailed` reflects the count — callers should surface this to
+ * the operator, and re-running adoption after clearing `merged_into_project`
+ * (or reseeding Chroma) is the recovery path.
  */
 export async function adoptMergedWorktrees(opts: {
   repoPath?: string;
@@ -201,6 +205,29 @@ export async function adoptMergedWorktrees(opts: {
     const { Database } = require('bun:sqlite') as typeof import('bun:sqlite');
     db = new Database(dbPath);
 
+    // Schema guard: adoption may be invoked on worker startup before
+    // DatabaseManager runs migrations. If the `merged_into_project` column
+    // isn't present yet, prepared statements below will fail with
+    // "no such column", silently skipping adoption until the next restart.
+    // Return early so the next boot (post-migration) picks this up.
+    interface ColumnInfo { name: string }
+    const obsColumns = db
+      .prepare('PRAGMA table_info(observations)')
+      .all() as ColumnInfo[];
+    const sumColumns = db
+      .prepare('PRAGMA table_info(session_summaries)')
+      .all() as ColumnInfo[];
+    const obsHasColumn = obsColumns.some(c => c.name === 'merged_into_project');
+    const sumHasColumn = sumColumns.some(c => c.name === 'merged_into_project');
+    if (!obsHasColumn || !sumHasColumn) {
+      logger.debug(
+        'SYSTEM',
+        'Worktree adoption skipped (merged_into_project column missing; will run after migration)',
+        { obsHasColumn, sumHasColumn }
+      );
+      return result;
+    }
+
     const selectObs = db.prepare(
       'SELECT id FROM observations WHERE project = ? AND merged_into_project IS NULL'
     );
@@ -290,3 +317,83 @@ export async function adoptMergedWorktrees(opts: {
 
   return result;
 }
+
+/**
+ * Run adoption once per distinct parent repo referenced by recorded cwds.
+ *
+ * Worker startup adoption cannot use `process.cwd()` as a seed — the daemon is
+ * spawned with cwd=marketplace-plugin-dir, which isn't a git repo. Instead, we
+ * derive candidate parent repos from `pending_messages.cwd` (the user's actual
+ * working directories), dedupe via `resolveMainRepoPath`, and run adoption
+ * against each. Failures on individual repos are logged but don't short-circuit
+ * the others.
+ *
+ * Safe to call before `dbManager.initialize()`: opens its own short-lived DB
+ * handle (readonly) to enumerate cwds, then delegates to `adoptMergedWorktrees`
+ * which opens its own writable handle.
+ */
+export async function adoptMergedWorktreesForAllKnownRepos(opts: {
+  dataDirectory?: string;
+  dryRun?: boolean;
+} = {}): Promise<AdoptionResult[]> {
+  const dataDirectory = opts.dataDirectory ?? DEFAULT_DATA_DIR;
+  const dbPath = path.join(dataDirectory, 'claude-mem.db');
+  const results: AdoptionResult[] = [];
+
+  if (!existsSync(dbPath)) {
+    logger.debug('SYSTEM', 'Worktree adoption skipped (no DB yet)', { dbPath });
+    return results;
+  }
+
+  const uniqueParents = new Set<string>();
+  let db: import('bun:sqlite').Database | null = null;
+  try {
+    const { Database } = require('bun:sqlite') as typeof import('bun:sqlite');
+    db = new Database(dbPath, { readonly: true });
+
+    const hasPending = db.prepare(
+      "SELECT name FROM sqlite_master WHERE type='table' AND name='pending_messages'"
+    ).get() as { name: string } | undefined;
+    if (!hasPending) {
+      logger.debug('SYSTEM', 'Worktree adoption skipped (pending_messages table missing)');
+      return results;
+    }
+
+    const cwdRows = db.prepare(`
+      SELECT cwd FROM pending_messages
+      WHERE cwd IS NOT NULL AND cwd != ''
+      GROUP BY cwd
+    `).all() as Array<{ cwd: string }>;
+
+    for (const { cwd } of cwdRows) {
+      const mainRepo = resolveMainRepoPath(cwd);
+      if (mainRepo) uniqueParents.add(mainRepo);
+    }
+  } finally {
+    db?.close();
+  }
+
+  if (uniqueParents.size === 0) {
+    logger.debug('SYSTEM', 'Worktree adoption found no known parent repos');
+    return results;
+  }
+
+  for (const repoPath of uniqueParents) {
+    try {
+      const result = await adoptMergedWorktrees({
+        repoPath,
+        dataDirectory,
+        dryRun: opts.dryRun
+      });
+      results.push(result);
+    } catch (err) {
+      logger.warn(
+        'SYSTEM',
+        'Worktree adoption failed for parent repo (continuing)',
+        { repoPath, error: err instanceof Error ? err.message : String(err) }
+      );
+    }
+  }
+
+  return results;
+}

src/services/sqlite/SessionStore.ts

@@ -1,5 +1,5 @@
 import { Database } from 'bun:sqlite';
-import { DATA_DIR, DB_PATH, ensureDir } from '../../shared/paths.js';
+import { DATA_DIR, DB_PATH, ensureDir, OBSERVER_SESSIONS_PROJECT } from '../../shared/paths.js';
 import { logger } from '../../utils/logger.js';
 import {
   TableColumnInfo,
@@ -65,6 +65,7 @@ export class SessionStore {
     this.addSessionCustomTitleColumn();
     this.addSessionPlatformSourceColumn();
     this.addObservationModelColumns();
+    this.ensureMergedIntoProjectColumns();
   }
 
   /**
@@ -944,6 +945,36 @@ export class SessionStore {
     this.db.prepare('INSERT OR IGNORE INTO schema_versions (version, applied_at) VALUES (?, ?)').run(26, new Date().toISOString());
   }
 
+  /**
+   * Ensure merged_into_project columns + indices exist on observations and session_summaries.
+   *
+   * Self-idempotent via PRAGMA table_info guard — does NOT bump schema_versions.
+   * Mirrors MigrationRunner.ensureMergedIntoProjectColumns so bundled artifacts
+   * that embed SessionStore (e.g. context-generator.cjs) stay schema-consistent
+   * with the standalone migration path.
+   */
+  private ensureMergedIntoProjectColumns(): void {
+    const obsCols = this.db
+      .query('PRAGMA table_info(observations)')
+      .all() as TableColumnInfo[];
+    if (!obsCols.some(c => c.name === 'merged_into_project')) {
+      this.db.run('ALTER TABLE observations ADD COLUMN merged_into_project TEXT');
+    }
+    this.db.run(
+      'CREATE INDEX IF NOT EXISTS idx_observations_merged_into ON observations(merged_into_project)'
+    );
+
+    const sumCols = this.db
+      .query('PRAGMA table_info(session_summaries)')
+      .all() as TableColumnInfo[];
+    if (!sumCols.some(c => c.name === 'merged_into_project')) {
+      this.db.run('ALTER TABLE session_summaries ADD COLUMN merged_into_project TEXT');
+    }
+    this.db.run(
+      'CREATE INDEX IF NOT EXISTS idx_summaries_merged_into ON session_summaries(merged_into_project)'
+    );
+  }
+
   /**
    * Update the memory session ID for a session
    * Called by SDKAgent when it captures the session ID from the first SDK message
@@ -1192,9 +1223,9 @@ export class SessionStore {
       SELECT DISTINCT project
       FROM sdk_sessions
       WHERE project IS NOT NULL AND project != ''
-        AND project != 'observer-sessions'
+        AND project != ?
     `;
-    const params: unknown[] = [];
+    const params: unknown[] = [OBSERVER_SESSIONS_PROJECT];
 
     if (normalizedPlatformSource) {
       query += ' AND COALESCE(platform_source, ?) = ?';
@@ -1219,10 +1250,10 @@ export class SessionStore {
         MAX(started_at_epoch) as latest_epoch
       FROM sdk_sessions
       WHERE project IS NOT NULL AND project != ''
-        AND project != 'observer-sessions'
+        AND project != ?
       GROUP BY COALESCE(platform_source, '${DEFAULT_PLATFORM_SOURCE}'), project
       ORDER BY latest_epoch DESC
-    `).all() as Array<{ platform_source: string; project: string; latest_epoch: number }>;
+    `).all(OBSERVER_SESSIONS_PROJECT) as Array<{ platform_source: string; project: string; latest_epoch: number }>;
 
     const projects: string[] = [];
     const seenProjects = new Set<string>();

src/services/sqlite/timeline/queries.ts

@@ -8,6 +8,7 @@
 import type { Database } from 'bun:sqlite';
 import type { ObservationRecord, SessionSummaryRecord, UserPromptRecord } from '../../../types/database.js';
 import { logger } from '../../../utils/logger.js';
+import { OBSERVER_SESSIONS_PROJECT } from '../../../shared/paths.js';
 
 /**
  * Timeline result containing observations, sessions, and prompts within a time window
@@ -210,10 +211,10 @@ export function getAllProjects(db: Database): string[] {
     SELECT DISTINCT project
     FROM sdk_sessions
     WHERE project IS NOT NULL AND project != ''
-      AND project != 'observer-sessions'
+      AND project != ?
     ORDER BY project ASC
   `);
 
-  const rows = stmt.all() as Array<{ project: string }>;
+  const rows = stmt.all(OBSERVER_SESSIONS_PROJECT) as Array<{ project: string }>;
   return rows.map(row => row.project);
 }

src/services/worker-service.ts

@@ -59,7 +59,7 @@ import {
   httpShutdown
 } from './infrastructure/HealthMonitor.js';
 import { performGracefulShutdown } from './infrastructure/GracefulShutdown.js';
-import { adoptMergedWorktrees } from './infrastructure/WorktreeAdoption.js';
+import { adoptMergedWorktrees, adoptMergedWorktreesForAllKnownRepos } from './infrastructure/WorktreeAdoption.js';
 
 // Server imports
 import { Server } from './server/Server.js';
@@ -368,13 +368,22 @@ export class WorkerService {
       // Stamp merged worktrees so their observations surface under the parent
       // project. Runs every startup (not marker-gated) because git state evolves
       // and the engine is fully idempotent. Must also precede dbManager.initialize().
+      //
+      // The worker daemon is spawned with cwd=marketplace-plugin-dir (not a git
+      // repo), so we can't seed adoption with process.cwd(). Instead, discover
+      // parent repos from recorded pending_messages.cwd values.
       try {
-        const adoption = await adoptMergedWorktrees({});
-        if (adoption.adoptedObservations > 0 || adoption.adoptedSummaries > 0 || adoption.chromaUpdates > 0) {
-          logger.info('SYSTEM', 'Merged worktrees adopted on startup', adoption);
-        }
-        if (adoption.errors.length > 0) {
-          logger.warn('SYSTEM', 'Worktree adoption had per-branch errors', { errors: adoption.errors });
+        const adoptions = await adoptMergedWorktreesForAllKnownRepos({});
+        for (const adoption of adoptions) {
+          if (adoption.adoptedObservations > 0 || adoption.adoptedSummaries > 0 || adoption.chromaUpdates > 0) {
+            logger.info('SYSTEM', 'Merged worktrees adopted on startup', adoption);
+          }
+          if (adoption.errors.length > 0) {
+            logger.warn('SYSTEM', 'Worktree adoption had per-branch errors', {
+              repoPath: adoption.repoPath,
+              errors: adoption.errors
+            });
+          }
         }
       } catch (err) {
         logger.error('SYSTEM', 'Worktree adoption failed (non-fatal)', {}, err as Error);

src/services/worker/PaginationHelper.ts

@@ -9,6 +9,7 @@
 
 import { DatabaseManager } from './DatabaseManager.js';
 import { logger } from '../../utils/logger.js';
+import { OBSERVER_SESSIONS_PROJECT } from '../../shared/paths.js';
 import type { PaginatedResult, Observation, Summary, UserPrompt } from '../worker-types.js';
 
 export class PaginationHelper {
@@ -107,7 +108,8 @@ export class PaginationHelper {
       params.push(project, project);
     } else {
       // Hide internal observer-session rows from the unfiltered UI list.
-      conditions.push("o.project != 'observer-sessions'");
+      conditions.push('o.project != ?');
+      params.push(OBSERVER_SESSIONS_PROJECT);
     }
     if (platformSource) {
       conditions.push(`COALESCE(s.platform_source, 'claude') = ?`);

src/shared/paths.ts

@@ -77,7 +77,7 @@ export const OBSERVER_SESSIONS_DIR = join(DATA_DIR, 'observer-sessions');
 
 // Project name assigned to observer sessions (basename of OBSERVER_SESSIONS_DIR).
 // UI queries filter this out so internal worker sessions don't pollute project lists.
-export const OBSERVER_SESSIONS_PROJECT = 'observer-sessions';
+export const OBSERVER_SESSIONS_PROJECT = basename(OBSERVER_SESSIONS_DIR);
 
 // Claude integration paths
 export const CLAUDE_SETTINGS_PATH = join(CLAUDE_CONFIG_DIR, 'settings.json');