Fix 6 bugs found during code review

- Fix NameError: pass state to _render_vace_settings (tab_batch_ng.py)
- Fix non-atomic sync_to_db: use BEGIN IMMEDIATE transaction with rollback
- Fix create_secondary() missing db/current_project/db_enabled fields
- Fix URL encoding: percent-encode project/file names in API URLs
- Fix import_json_file crash on re-import: upsert instead of insert
- Fix dual DB instances: share single ProjectDB between UI and API routes
- Also fixes top_level metadata never being updated on existing data_files

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

state.py

@@ -34,4 +34,7 @@ class AppState:
             config=self.config,
             current_dir=self.current_dir,
             snippets=self.snippets,
+            db=self.db,
+            current_project=self.current_project,
+            db_enabled=self.db_enabled,
         )