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/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>();