fix: prompts call MCP tools directly, sync handles semantic errors, status uses local routing

- Prompts (search, continue_conversation) now call MCP tools directly
  instead of going through API endpoints, matching the recent_activity
  pattern and fixing #526 where prompts returned empty results
- sync_file catches SemanticDependenciesMissingError separately so
  entities are still returned successfully when vector embedding fails,
  with a clear warning instead of silent failure (#578)
- `bm status` and `bm doctor` default to local routing since they scan
  the local filesystem — cloud routing returned Docker-internal paths

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Signed-off-by: phernandez <paul@basicmachines.co>

src/basic_memory/cli/commands/doctor.py

@@ -139,6 +139,9 @@ def doctor(
     """Run local consistency checks to verify file/database sync."""
     try:
         validate_routing_flags(local, cloud)
+        # Doctor runs local filesystem checks — always default to local routing
+        if not local and not cloud:
+            local = True
         with force_routing(local=local, cloud=cloud):
             run_with_cleanup(run_doctor())
     except (ToolError, ValueError) as e:

src/basic_memory/cli/commands/status.py

@@ -179,6 +179,13 @@ def status(
 
     try:
         validate_routing_flags(local, cloud)
+        # Trigger: no explicit routing flag provided
+        # Why: status scans the local filesystem — cloud routing would use the
+        #      Docker-internal path stored in the cloud database, which doesn't
+        #      exist locally.
+        # Outcome: default to local routing unless --cloud was explicitly requested.
+        if not local and not cloud:
+            local = True
         with force_routing(local=local, cloud=cloud):
             run_with_cleanup(run_status(project, verbose))  # pragma: no cover
     except ValueError as e: