fix(worktree): address CodeRabbit PR review feedback

- Document --branch override in npx-cli help text
- Guard ContextBuilder against empty projects[] override; fall back to cwd-derived primary
- Ensure merged_into_project indexes are created even if ALTER ran in a prior partial migration
- Reject adopt --branch/--cwd flags with missing or flag-like values
- Use defined --color-border-primary token for merged badge border

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

src/services/sqlite/migrations/runner.ts

@@ -937,19 +937,19 @@ export class MigrationRunner {
       .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)'
-      );
     }
+    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)'
-      );
     }
+    this.db.run(
+      'CREATE INDEX IF NOT EXISTS idx_summaries_merged_into ON session_summaries(merged_into_project)'
+    );
   }
 }