Fix setup persistence and load persisted runtime configuration

backend/app/startup.py

@@ -24,6 +24,15 @@ from app.utils.setup_state import set_setup_complete_cache
 log: structlog.stdlib.BoundLogger = structlog.get_logger()
 
 
+async def _ensure_database_schema(database_path: str) -> None:
+    """Create the configured runtime database if it does not already exist."""
+    db = await open_db(database_path)
+    try:
+        await init_db(db)
+    finally:
+        await db.close()
+
+
 async def startup_shared_resources(
     app: FastAPI,
     settings: Settings,
@@ -44,6 +53,7 @@ async def startup_shared_resources(
 
     log.debug("database_directory_ensured", directory=str(db_path.parent))
 
+    original_db_path = db_path.resolve()
     startup_db = await open_db(settings.database_path)
     try:
         await init_db(startup_db)
@@ -52,6 +62,20 @@ async def startup_shared_resources(
         setup_complete = await setup_service.is_setup_complete(startup_db)
         set_setup_complete_cache(app, setup_complete)
         log.debug("setup_completion_cached", completed=setup_complete)
+
+        if setup_complete:
+            persisted_runtime_settings = (
+                await setup_service.get_persisted_runtime_settings(startup_db)
+            )
+            if persisted_runtime_settings:
+                updated_settings = settings.model_copy(update=persisted_runtime_settings)
+                if Path(updated_settings.database_path).resolve() != original_db_path:
+                    await _ensure_database_schema(updated_settings.database_path)
+                app.state.settings = updated_settings
+                log.info(
+                    "runtime_settings_overridden_from_setup",
+                    overrides=persisted_runtime_settings,
+                )
     finally:
         await startup_db.close()