logs: migrate to molecular CoT JSON protocol, fix regressions

- Replace BeliefFormatter with CotJsonFormatter (single-line JSON with
  ts, level, trace_id, src, marker, intent, payload, error, span_id)
- Migrate belief_scope to use cot_log() for structured JSON output
- Update monkey-patched reason/reflect/explore to pass extra= dict
- Strip 200+ inline [REASON]/[REFLECT]/[EXPLORE] markers from 50+ files
- Remove belief_scope from hot-path utilities (_parse_datetime,
  _json_load_if_needed) to eliminate startup log noise
- Register TraceContextMiddleware in app.py (was implemented but unused)
- Seed trace_id in startup_event/shutdown_event for background tasks
- Fix broken relative imports in translate routes (3 dots → 4 dots)
- Migrate 43 translate_routes log calls to logger.reason/explore
- Fix SyntaxError (positional arg after extra=) in _repo_operations_routes
- Fix IndentationError in rbac_permission_catalog except-block
- Add smoke test tests/test_smoke_app.py (catches import errors before run)

backend/src/plugins/storage/plugin.py

@@ -186,7 +186,7 @@ class StoragePlugin(PluginBase):
                 # Use singular name for consistency with BackupPlugin and GitService
                 path = root / category.value
                 path.mkdir(parents=True, exist_ok=True)
-                logger.debug(f"[StoragePlugin][REASON] Ensured directory: {path}")
+                logger.reason(f"Ensured directory: {path}", extra={"src": "StoragePlugin.ensure_directories"})
     # [/DEF:ensure_directories:Function]
 
     # [DEF:validate_path:Function]
@@ -221,8 +221,9 @@ class StoragePlugin(PluginBase):
     ) -> List[StoredFile]:
         with belief_scope("StoragePlugin:list_files"):
             root = self.get_storage_root()
-            logger.info(
-                f"[StoragePlugin][REASON] Listing files in root: {root}, category: {category}, subpath: {subpath}, recursive: {recursive}"
+            logger.reason(
+                f"Listing files in root: {root}",
+                extra={"src": "StoragePlugin.list_files", "payload": {"root": str(root), "category": category.value if category else None, "subpath": subpath, "recursive": recursive}},
             )
             files = []
 
@@ -258,7 +259,7 @@ class StoragePlugin(PluginBase):
                 if not target_dir.exists():
                     continue
                 
-                logger.debug(f"[StoragePlugin][REASON] Scanning directory: {target_dir}")
+                logger.reason(f"Scanning directory: {target_dir}", extra={"src": "StoragePlugin.list_files"})
 
                 if recursive:
                     for current_root, dirs, filenames in os.walk(target_dir):
@@ -358,7 +359,7 @@ class StoragePlugin(PluginBase):
                     shutil.rmtree(full_path)
                 else:
                     full_path.unlink()
-                logger.info(f"[StoragePlugin][REASON] Deleted: {full_path}")
+                logger.reason(f"Deleted: {full_path}", extra={"src": "StoragePlugin.delete_file"})
             else:
                 raise FileNotFoundError(f"Item {path} not found")
     # [/DEF:delete_file:Function]