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/services/git/_sync.py

@@ -60,9 +60,9 @@ class GitServiceSyncMixin:
                 finally:
                     session.close()
             except Exception as diag_error:
-                logger.warning(
-                    "[push_changes][REASON] Failed to load repository binding diagnostics for dashboard %s: %s",
-                    dashboard_id, diag_error,
+                logger.reason(
+                    "Failed to load repository binding diagnostics",
+                    extra={"src": "push_changes", "dashboard_id": dashboard_id, "error": str(diag_error)},
                 )
             realigned_origin_url = self._align_origin_host_with_config(
                 dashboard_id=dashboard_id,
@@ -75,13 +75,13 @@ class GitServiceSyncMixin:
                 origin_urls = list(origin.urls)
             except Exception:
                 origin_urls = []
-            logger.info(
-                "[push_changes][REASON] Push diagnostics dashboard=%s config_id=%s config_url=%s binding_remote_url=%s origin_urls=%s origin_realigned=%s",
-                dashboard_id, binding_config_id, binding_config_url, binding_remote_url, origin_urls, bool(realigned_origin_url),
+            logger.reason(
+                f"Push diagnostics dashboard={dashboard_id} config_id={binding_config_id} config_url={binding_config_url} binding_remote_url={binding_remote_url} origin_urls={origin_urls} origin_realigned={bool(realigned_origin_url)}",
+                extra={"src": "push_changes"},
             )
             try:
                 current_branch = repo.active_branch
-                logger.info(f"[push_changes][REASON] Pushing branch {current_branch.name} to origin")
+                logger.reason(f"Pushing branch {current_branch.name} to origin", extra={"src": "push_changes"})
                 tracking_branch = None
                 try:
                     tracking_branch = current_branch.tracking_branch()
@@ -120,10 +120,9 @@ class GitServiceSyncMixin:
             merge_head_path = os.path.join(repo.git_dir, "MERGE_HEAD")
             if os.path.exists(merge_head_path):
                 payload = self._build_unfinished_merge_payload(repo)
-                logger.warning(
-                    "[pull_changes][REASON] Unfinished merge detected for dashboard %s (repo_path=%s git_dir=%s branch=%s merge_head=%s merge_msg=%s)",
-                    dashboard_id, payload["repository_path"], payload["git_dir"],
-                    payload["current_branch"], payload["merge_head"], payload["merge_message_preview"],
+                logger.reason(
+                    f"Unfinished merge detected for dashboard {dashboard_id} (repo_path={payload['repository_path']} git_dir={payload['git_dir']} branch={payload['current_branch']} merge_head={payload['merge_head']} merge_msg={payload['merge_message_preview']})",
+                    extra={"src": "pull_changes"},
                 )
                 raise HTTPException(status_code=409, detail=payload)
             try:
@@ -133,23 +132,23 @@ class GitServiceSyncMixin:
                     origin_urls = list(origin.urls)
                 except Exception:
                     origin_urls = []
-                logger.info(
-                    "[pull_changes][REASON] Pull diagnostics dashboard=%s repo_path=%s branch=%s origin_urls=%s",
-                    dashboard_id, repo.working_tree_dir, current_branch, origin_urls,
+                logger.reason(
+                    f"Pull diagnostics dashboard={dashboard_id} repo_path={repo.working_tree_dir} branch={current_branch} origin_urls={origin_urls}",
+                    extra={"src": "pull_changes"},
                 )
                 origin.fetch(prune=True)
                 remote_ref = f"origin/{current_branch}"
                 has_remote_branch = any(ref.name == remote_ref for ref in repo.refs)
-                logger.info(
-                    "[pull_changes][REASON] Pull remote branch check dashboard=%s branch=%s remote_ref=%s exists=%s",
-                    dashboard_id, current_branch, remote_ref, has_remote_branch,
+                logger.reason(
+                    f"Pull remote branch check dashboard={dashboard_id} branch={current_branch} remote_ref={remote_ref} exists={has_remote_branch}",
+                    extra={"src": "pull_changes"},
                 )
                 if not has_remote_branch:
                     raise HTTPException(
                         status_code=409,
                         detail=f"Remote branch '{current_branch}' does not exist yet. Push this branch first.",
                     )
-                logger.info(f"[pull_changes][REASON] Pulling changes from origin/{current_branch}")
+                logger.reason(f"Pulling changes from origin/{current_branch}", extra={"src": "pull_changes"})
                 repo.git.pull("--no-rebase", "origin", current_branch)
             except ValueError:
                 logger.error(f"[pull_changes][Coherence:Failed] Remote 'origin' not found for dashboard {dashboard_id}")