fix: scope entity queries by project_id in upsert_entity method

Replace direct select(Entity) calls with self.select() to ensure proper
project filtering in the upsert_entity method. This prevents "multiple rows"
errors when similar permalinks exist across different projects.

Fixes issue where:
- File sync fails with "Multiple rows were found when one or none was required" 
- Similar permalinks across projects (e.g., "foo" and "foo-complete") cause conflicts
- Queries were not properly scoped by project_id constraint

Changed in EntityRepository.upsert_entity():
- Query after entity update (lines 144-148)
- Query after entity insert (lines 164-168)  
- Query after race condition update (lines 205-210)
- Query after permalink conflict resolution (lines 245-249)

Co-authored-by: Drew Cain <groksrc@users.noreply.github.com>

Author: claude[bot]

src/basic_memory/repository/entity_repository.py

@@ -142,7 +142,7 @@ async def upsert_entity(self, entity: Entity) -> Entity:
                 await session.flush()
                 # Return with relationships loaded
                 query = (
-                    select(Entity)
+                    self.select()
                     .where(Entity.file_path == entity.file_path)
                     .options(*self.get_load_options())
                 )
@@ -162,7 +162,7 @@ async def upsert_entity(self, entity: Entity) -> Entity:
 
                 # Return with relationships loaded
                 query = (
-                    select(Entity)
+                    self.select()
                     .where(Entity.file_path == entity.file_path)
                     .options(*self.get_load_options())
                 )
@@ -203,7 +203,7 @@ async def upsert_entity(self, entity: Entity) -> Entity:
                     await session.flush()
                     # Return the updated entity with relationships loaded
                     query = (
-                        select(Entity)
+                        self.select()
                         .where(Entity.file_path == entity.file_path)
                         .options(*self.get_load_options())
                     )
@@ -243,7 +243,7 @@ async def _handle_permalink_conflict(self, entity: Entity, session: AsyncSession
 
         # Return the inserted entity with relationships loaded
         query = (
-            select(Entity)
+            self.select()
             .where(Entity.file_path == entity.file_path)
             .options(*self.get_load_options())
         )