basic-memory 0.7.0__py3-none-any.whl → 0.17.4__py3-none-any.whl

basic_memory/services/entity_service.py

@@ -1,24 +1,35 @@
 """Service for managing entities in the database."""
 
 from pathlib import Path
-from typing import Sequence, List, Optional, Tuple, Union
+from typing import List, Optional, Sequence, Tuple, Union
 
 import frontmatter
+import yaml
 from loguru import logger
 from sqlalchemy.exc import IntegrityError
 
+
+from basic_memory.config import ProjectConfig, BasicMemoryConfig
+from basic_memory.file_utils import (
+    has_frontmatter,
+    parse_frontmatter,
+    remove_frontmatter,
+    dump_frontmatter,
+)
 from basic_memory.markdown import EntityMarkdown
+from basic_memory.markdown.entity_parser import EntityParser
 from basic_memory.markdown.utils import entity_model_from_markdown, schema_to_markdown
-from basic_memory.models import Entity as EntityModel, Observation, Relation
+from basic_memory.models import Entity as EntityModel
+from basic_memory.models import Observation, Relation
+from basic_memory.models.knowledge import Entity
 from basic_memory.repository import ObservationRepository, RelationRepository
 from basic_memory.repository.entity_repository import EntityRepository
 from basic_memory.schemas import Entity as EntitySchema
 from basic_memory.schemas.base import Permalink
-from basic_memory.services.exceptions import EntityNotFoundError, EntityCreationError
-from basic_memory.services import FileService
-from basic_memory.services import BaseService
+from basic_memory.services import BaseService, FileService
+from basic_memory.services.exceptions import EntityCreationError, EntityNotFoundError
 from basic_memory.services.link_resolver import LinkResolver
-from basic_memory.markdown.entity_parser import EntityParser
+from basic_memory.services.search_service import SearchService
 from basic_memory.utils import generate_permalink
 
 
@@ -33,6 +44,8 @@ class EntityService(BaseService[EntityModel]):
         relation_repository: RelationRepository,
         file_service: FileService,
         link_resolver: LinkResolver,
+        search_service: Optional[SearchService] = None,
+        app_config: Optional[BasicMemoryConfig] = None,
     ):
         super().__init__(entity_repository)
         self.observation_repository = observation_repository
@@ -40,9 +53,53 @@ class EntityService(BaseService[EntityModel]):
         self.entity_parser = entity_parser
         self.file_service = file_service
         self.link_resolver = link_resolver
+        self.search_service = search_service
+        self.app_config = app_config
+
+    async def detect_file_path_conflicts(
+        self, file_path: str, skip_check: bool = False
+    ) -> List[Entity]:
+        """Detect potential file path conflicts for a given file path.
+
+        This checks for entities with similar file paths that might cause conflicts:
+        - Case sensitivity differences (Finance/file.md vs finance/file.md)
+        - Character encoding differences
+        - Hyphen vs space differences
+        - Unicode normalization differences
+
+        Args:
+            file_path: The file path to check for conflicts
+            skip_check: If True, skip the check and return empty list (optimization for bulk operations)
+
+        Returns:
+            List of entities that might conflict with the given file path
+        """
+        if skip_check:
+            return []
+
+        from basic_memory.utils import detect_potential_file_conflicts
+
+        conflicts = []
+
+        # Get all existing file paths
+        all_entities = await self.repository.find_all()
+        existing_paths = [entity.file_path for entity in all_entities]
+
+        # Use the enhanced conflict detection utility
+        conflicting_paths = detect_potential_file_conflicts(file_path, existing_paths)
+
+        # Find the entities corresponding to conflicting paths
+        for entity in all_entities:
+            if entity.file_path in conflicting_paths:
+                conflicts.append(entity)
+
+        return conflicts
 
     async def resolve_permalink(
-        self, file_path: Permalink | Path, markdown: Optional[EntityMarkdown] = None
+        self,
+        file_path: Permalink | Path,
+        markdown: Optional[EntityMarkdown] = None,
+        skip_conflict_check: bool = False,
     ) -> str:
         """Get or generate unique permalink for an entity.
 
@@ -51,31 +108,53 @@ class EntityService(BaseService[EntityModel]):
         2. If markdown has permalink but it's used by another file -> make unique
         3. For existing files, keep current permalink from db
         4. Generate new unique permalink from file path
+
+        Enhanced to detect and handle character-related conflicts.
+
+        Note: Uses lightweight repository methods that skip eager loading of
+        observations and relations for better performance during bulk operations.
         """
+        file_path_str = Path(file_path).as_posix()
+
+        # Check for potential file path conflicts before resolving permalink
+        conflicts = await self.detect_file_path_conflicts(
+            file_path_str, skip_check=skip_conflict_check
+        )
+        if conflicts:
+            logger.warning(
+                f"Detected potential file path conflicts for '{file_path_str}': "
+                f"{[entity.file_path for entity in conflicts]}"
+            )
+
         # If markdown has explicit permalink, try to validate it
         if markdown and markdown.frontmatter.permalink:
             desired_permalink = markdown.frontmatter.permalink
-            existing = await self.repository.get_by_permalink(desired_permalink)
+            # Use lightweight method - we only need to check file_path
+            existing_file_path = await self.repository.get_file_path_for_permalink(
+                desired_permalink
+            )
 
             # If no conflict or it's our own file, use as is
-            if not existing or existing.file_path == str(file_path):
+            if not existing_file_path or existing_file_path == file_path_str:
                 return desired_permalink
 
         # For existing files, try to find current permalink
-        existing = await self.repository.get_by_file_path(str(file_path))
-        if existing:
-            return existing.permalink
+        # Use lightweight method - we only need the permalink
+        existing_permalink = await self.repository.get_permalink_for_file_path(file_path_str)
+        if existing_permalink:
+            return existing_permalink
 
         # New file - generate permalink
         if markdown and markdown.frontmatter.permalink:
             desired_permalink = markdown.frontmatter.permalink
         else:
-            desired_permalink = generate_permalink(file_path)
+            desired_permalink = generate_permalink(file_path_str)
 
-        # Make unique if needed
+        # Make unique if needed - enhanced to handle character conflicts
+        # Use lightweight existence check instead of loading full entity
         permalink = desired_permalink
         suffix = 1
-        while await self.repository.get_by_permalink(permalink):
+        while await self.repository.permalink_exists(permalink):
             permalink = f"{desired_permalink}-{suffix}"
             suffix += 1
             logger.debug(f"creating unique permalink: {permalink}")
@@ -86,13 +165,18 @@ class EntityService(BaseService[EntityModel]):
         """Create new entity or update existing one.
         Returns: (entity, is_new) where is_new is True if a new entity was created
         """
-        logger.debug(f"Creating or updating entity: {schema}")
+        logger.debug(
+            f"Creating or updating entity: {schema.file_path}, permalink: {schema.permalink}"
+        )
 
-        # Try to find existing entity using smart resolution
-        existing = await self.link_resolver.resolve_link(schema.permalink)
+        # Try to find existing entity using strict resolution (no fuzzy search)
+        # This prevents incorrectly matching similar file paths like "Node A.md" and "Node C.md"
+        existing = await self.link_resolver.resolve_link(schema.file_path, strict=True)
+        if not existing and schema.permalink:
+            existing = await self.link_resolver.resolve_link(schema.permalink, strict=True)
 
         if existing:
-            logger.debug(f"Found existing entity: {existing.permalink}")
+            logger.debug(f"Found existing entity: {existing.file_path}")
             return await self.update_entity(existing, schema), False
         else:
             # Create new entity
@@ -100,7 +184,7 @@ class EntityService(BaseService[EntityModel]):
 
     async def create_entity(self, schema: EntitySchema) -> EntityModel:
         """Create a new entity and write to filesystem."""
-        logger.debug(f"Creating entity: {schema.permalink}")
+        logger.debug(f"Creating entity: {schema.title}")
 
         # Get file path and ensure it's a Path object
         file_path = Path(schema.file_path)
@@ -110,71 +194,181 @@ class EntityService(BaseService[EntityModel]):
                 f"file for entity {schema.folder}/{schema.title} already exists: {file_path}"
             )
 
-        # Get unique permalink
-        permalink = await self.resolve_permalink(schema.permalink or file_path)
-        schema._permalink = permalink
+        # Parse content frontmatter to check for user-specified permalink and entity_type
+        content_markdown = None
+        if schema.content and has_frontmatter(schema.content):
+            content_frontmatter = parse_frontmatter(schema.content)
+
+            # If content has entity_type/type, use it to override the schema entity_type
+            if "type" in content_frontmatter:
+                schema.entity_type = content_frontmatter["type"]
+
+            if "permalink" in content_frontmatter:
+                # Create a minimal EntityMarkdown object for permalink resolution
+                from basic_memory.markdown.schemas import EntityFrontmatter
+
+                frontmatter_metadata = {
+                    "title": schema.title,
+                    "type": schema.entity_type,
+                    "permalink": content_frontmatter["permalink"],
+                }
+                frontmatter_obj = EntityFrontmatter(metadata=frontmatter_metadata)
+                content_markdown = EntityMarkdown(
+                    frontmatter=frontmatter_obj,
+                    content="",  # content not needed for permalink resolution
+                    observations=[],
+                    relations=[],
+                )
+
+        # Get unique permalink (prioritizing content frontmatter) unless disabled
+        if self.app_config and self.app_config.disable_permalinks:
+            # Use empty string as sentinel to indicate permalinks are disabled
+            # The permalink property will return None when it sees empty string
+            schema._permalink = ""
+        else:
+            # Generate and set permalink
+            permalink = await self.resolve_permalink(file_path, content_markdown)
+            schema._permalink = permalink
 
         post = await schema_to_markdown(schema)
 
         # write file
-        final_content = frontmatter.dumps(post, sort_keys=False)
+        final_content = dump_frontmatter(post)
         checksum = await self.file_service.write_file(file_path, final_content)
 
-        # parse entity from file
-        entity_markdown = await self.entity_parser.parse_file(file_path)
+        # parse entity from content we just wrote (avoids re-reading file for cloud compatibility)
+        entity_markdown = await self.entity_parser.parse_markdown_content(
+            file_path=file_path,
+            content=final_content,
+        )
 
         # create entity
-        await self.create_entity_from_markdown(file_path, entity_markdown)
+        created = await self.create_entity_from_markdown(file_path, entity_markdown)
 
         # add relations
-        entity = await self.update_entity_relations(file_path, entity_markdown)
+        entity = await self.update_entity_relations(created.file_path, entity_markdown)
 
         # Set final checksum to mark complete
         return await self.repository.update(entity.id, {"checksum": checksum})
 
     async def update_entity(self, entity: EntityModel, schema: EntitySchema) -> EntityModel:
         """Update an entity's content and metadata."""
-        logger.debug(f"Updating entity with permalink: {entity.permalink}")
+        logger.debug(
+            f"Updating entity with permalink: {entity.permalink} content-type: {schema.content_type}"
+        )
 
         # Convert file path string to Path
         file_path = Path(entity.file_path)
 
+        # Read existing content via file_service (for cloud compatibility)
+        existing_content = await self.file_service.read_file_content(file_path)
+        existing_markdown = await self.entity_parser.parse_markdown_content(
+            file_path=file_path,
+            content=existing_content,
+        )
+
+        # Parse content frontmatter to check for user-specified permalink and entity_type
+        content_markdown = None
+        if schema.content and has_frontmatter(schema.content):
+            content_frontmatter = parse_frontmatter(schema.content)
+
+            # If content has entity_type/type, use it to override the schema entity_type
+            if "type" in content_frontmatter:
+                schema.entity_type = content_frontmatter["type"]
+
+            if "permalink" in content_frontmatter:
+                # Create a minimal EntityMarkdown object for permalink resolution
+                from basic_memory.markdown.schemas import EntityFrontmatter
+
+                frontmatter_metadata = {
+                    "title": schema.title,
+                    "type": schema.entity_type,
+                    "permalink": content_frontmatter["permalink"],
+                }
+                frontmatter_obj = EntityFrontmatter(metadata=frontmatter_metadata)
+                content_markdown = EntityMarkdown(
+                    frontmatter=frontmatter_obj,
+                    content="",  # content not needed for permalink resolution
+                    observations=[],
+                    relations=[],
+                )
+
+        # Check if we need to update the permalink based on content frontmatter (unless disabled)
+        new_permalink = entity.permalink  # Default to existing
+        if self.app_config and not self.app_config.disable_permalinks:
+            if content_markdown and content_markdown.frontmatter.permalink:
+                # Resolve permalink with the new content frontmatter
+                resolved_permalink = await self.resolve_permalink(file_path, content_markdown)
+                if resolved_permalink != entity.permalink:
+                    new_permalink = resolved_permalink
+                    # Update the schema to use the new permalink
+                    schema._permalink = new_permalink
+
+        # Create post with new content from schema
         post = await schema_to_markdown(schema)
 
+        # Merge new metadata with existing metadata
+        existing_markdown.frontmatter.metadata.update(post.metadata)
+
+        # Ensure the permalink in the metadata is the resolved one
+        if new_permalink != entity.permalink:
+            existing_markdown.frontmatter.metadata["permalink"] = new_permalink
+
+        # Create a new post with merged metadata
+        merged_post = frontmatter.Post(post.content, **existing_markdown.frontmatter.metadata)
+
         # write file
-        final_content = frontmatter.dumps(post)
+        final_content = dump_frontmatter(merged_post)
         checksum = await self.file_service.write_file(file_path, final_content)
 
-        # parse entity from file
-        entity_markdown = await self.entity_parser.parse_file(file_path)
+        # parse entity from content we just wrote (avoids re-reading file for cloud compatibility)
+        entity_markdown = await self.entity_parser.parse_markdown_content(
+            file_path=file_path,
+            content=final_content,
+        )
 
         # update entity in db
         entity = await self.update_entity_and_observations(file_path, entity_markdown)
 
         # add relations
-        await self.update_entity_relations(file_path, entity_markdown)
+        await self.update_entity_relations(file_path.as_posix(), entity_markdown)
 
         # Set final checksum to match file
         entity = await self.repository.update(entity.id, {"checksum": checksum})
 
         return entity
 
-    async def delete_entity(self, permalink: str) -> bool:
+    async def delete_entity(self, permalink_or_id: str | int) -> bool:
         """Delete entity and its file."""
-        logger.debug(f"Deleting entity: {permalink}")
+        logger.debug(f"Deleting entity: {permalink_or_id}")
 
         try:
             # Get entity first for file deletion
-            entity = await self.get_by_permalink(permalink)
-
-            # Delete file first
+            if isinstance(permalink_or_id, str):
+                entity = await self.get_by_permalink(permalink_or_id)
+            else:
+                entities = await self.get_entities_by_id([permalink_or_id])
+                if len(entities) != 1:  # pragma: no cover
+                    logger.error(
+                        "Entity lookup error", entity_id=permalink_or_id, found_count=len(entities)
+                    )
+                    raise ValueError(
+                        f"Expected 1 entity with ID {permalink_or_id}, got {len(entities)}"
+                    )
+                entity = entities[0]
+
+            # Delete from search index first (if search_service is available)
+            if self.search_service:
+                await self.search_service.handle_delete(entity)
+
+            # Delete file
             await self.file_service.delete_entity_file(entity)
 
             # Delete from DB (this will cascade to observations/relations)
             return await self.repository.delete(entity.id)
 
         except EntityNotFoundError:
-            logger.info(f"Entity not found: {permalink}")
+            logger.info(f"Entity not found: {permalink_or_id}")
             return True  # Already deleted
 
     async def get_by_permalink(self, permalink: str) -> EntityModel:
@@ -206,13 +400,23 @@ class EntityService(BaseService[EntityModel]):
 
         Creates the entity with null checksum to indicate sync not complete.
         Relations will be added in second pass.
+
+        Uses UPSERT approach to handle permalink/file_path conflicts cleanly.
         """
-        logger.debug(f"Creating entity: {markdown.frontmatter.title}")
-        model = entity_model_from_markdown(file_path, markdown)
+        logger.debug(f"Creating entity: {markdown.frontmatter.title} file_path: {file_path}")
+        model = entity_model_from_markdown(
+            file_path, markdown, project_id=self.repository.project_id
+        )
 
         # Mark as incomplete because we still need to add relations
         model.checksum = None
-        return await self.repository.add(model)
+
+        # Use UPSERT to handle conflicts cleanly
+        try:
+            return await self.repository.upsert_entity(model)
+        except Exception as e:
+            logger.error(f"Failed to upsert entity for {file_path}: {e}")
+            raise EntityCreationError(f"Failed to create entity: {str(e)}") from e
 
     async def update_entity_and_observations(
         self, file_path: Path, markdown: EntityMarkdown
@@ -224,7 +428,7 @@ class EntityService(BaseService[EntityModel]):
         """
         logger.debug(f"Updating entity and observations: {file_path}")
 
-        db_entity = await self.repository.get_by_file_path(str(file_path))
+        db_entity = await self.repository.get_by_file_path(file_path.as_posix())
 
         # Clear observations for entity
         await self.observation_repository.delete_by_fields(entity_id=db_entity.id)
@@ -232,6 +436,7 @@ class EntityService(BaseService[EntityModel]):
         # add new observations
         observations = [
             Observation(
+                project_id=self.observation_repository.project_id,
                 entity_id=db_entity.id,
                 content=obs.content,
                 category=obs.category,
@@ -256,44 +461,404 @@ class EntityService(BaseService[EntityModel]):
 
     async def update_entity_relations(
         self,
-        file_path: Path,
+        path: str,
         markdown: EntityMarkdown,
     ) -> EntityModel:
         """Update relations for entity"""
-        logger.debug(f"Updating relations for entity: {file_path}")
+        logger.debug(f"Updating relations for entity: {path}")
 
-        db_entity = await self.repository.get_by_file_path(str(file_path))
+        db_entity = await self.repository.get_by_file_path(path)
 
         # Clear existing relations first
         await self.relation_repository.delete_outgoing_relations_from_entity(db_entity.id)
 
-        # Process each relation
-        for rel in markdown.relations:
-            # Resolve the target permalink
-            target_entity = await self.link_resolver.resolve_link(
-                rel.target,
-            )
+        # Batch resolve all relation targets in parallel
+        if markdown.relations:
+            import asyncio
+
+            # Create tasks for all relation lookups
+            # Use strict=True to disable fuzzy search - only exact matches should create resolved relations
+            # This ensures forward references (links to non-existent entities) remain unresolved (to_id=NULL)
+            lookup_tasks = [
+                self.link_resolver.resolve_link(rel.target, strict=True)
+                for rel in markdown.relations
+            ]
+
+            # Execute all lookups in parallel
+            resolved_entities = await asyncio.gather(*lookup_tasks, return_exceptions=True)
+
+            # Process results and create relation records
+            relations_to_add = []
+            for rel, resolved in zip(markdown.relations, resolved_entities):
+                # Handle exceptions from gather and None results
+                target_entity: Optional[Entity] = None
+                if not isinstance(resolved, Exception):
+                    # Type narrowing: resolved is Optional[Entity] here, not Exception
+                    target_entity = resolved  # type: ignore
+
+                # if the target is found, store the id
+                target_id = target_entity.id if target_entity else None
+                # if the target is found, store the title, otherwise add the target for a "forward link"
+                target_name = target_entity.title if target_entity else rel.target
+
+                # Create the relation
+                relation = Relation(
+                    project_id=self.relation_repository.project_id,
+                    from_id=db_entity.id,
+                    to_id=target_id,
+                    to_name=target_name,
+                    relation_type=rel.type,
+                    context=rel.context,
+                )
+                relations_to_add.append(relation)
+
+            # Batch insert all relations
+            if relations_to_add:
+                try:
+                    await self.relation_repository.add_all(relations_to_add)
+                except IntegrityError:
+                    # Some relations might be duplicates - fall back to individual inserts
+                    logger.debug("Batch relation insert failed, trying individual inserts")
+                    for relation in relations_to_add:
+                        try:
+                            await self.relation_repository.add(relation)
+                        except IntegrityError:
+                            # Unique constraint violation - relation already exists
+                            logger.debug(
+                                f"Skipping duplicate relation {relation.relation_type} from {db_entity.permalink}"
+                            )
+                            continue
+
+        return await self.repository.get_by_file_path(path)
+
+    async def edit_entity(
+        self,
+        identifier: str,
+        operation: str,
+        content: str,
+        section: Optional[str] = None,
+        find_text: Optional[str] = None,
+        expected_replacements: int = 1,
+    ) -> EntityModel:
+        """Edit an existing entity's content using various operations.
+
+        Args:
+            identifier: Entity identifier (permalink, title, etc.)
+            operation: The editing operation (append, prepend, find_replace, replace_section)
+            content: The content to add or use for replacement
+            section: For replace_section operation - the markdown header
+            find_text: For find_replace operation - the text to find and replace
+            expected_replacements: For find_replace operation - expected number of replacements (default: 1)
+
+        Returns:
+            The updated entity model
+
+        Raises:
+            EntityNotFoundError: If the entity cannot be found
+            ValueError: If required parameters are missing for the operation or replacement count doesn't match expected
+        """
+        logger.debug(f"Editing entity: {identifier}, operation: {operation}")
+
+        # Find the entity using the link resolver with strict mode for destructive operations
+        entity = await self.link_resolver.resolve_link(identifier, strict=True)
+        if not entity:
+            raise EntityNotFoundError(f"Entity not found: {identifier}")
+
+        # Read the current file content
+        file_path = Path(entity.file_path)
+        current_content, _ = await self.file_service.read_file(file_path)
+
+        # Apply the edit operation
+        new_content = self.apply_edit_operation(
+            current_content, operation, content, section, find_text, expected_replacements
+        )
 
-            # if the target is found, store the id
-            target_id = target_entity.id if target_entity else None
-            # if the target is found, store the title, otherwise add the target for a "forward link"
-            target_name = target_entity.title if target_entity else rel.target
-
-            # Create the relation
-            relation = Relation(
-                from_id=db_entity.id,
-                to_id=target_id,
-                to_name=target_name,
-                relation_type=rel.type,
-                context=rel.context,
+        # Write the updated content back to the file
+        checksum = await self.file_service.write_file(file_path, new_content)
+
+        # Parse the content we just wrote (avoids re-reading file for cloud compatibility)
+        entity_markdown = await self.entity_parser.parse_markdown_content(
+            file_path=file_path,
+            content=new_content,
+        )
+
+        # Update entity and its relationships
+        entity = await self.update_entity_and_observations(file_path, entity_markdown)
+        await self.update_entity_relations(file_path.as_posix(), entity_markdown)
+
+        # Set final checksum to match file
+        entity = await self.repository.update(entity.id, {"checksum": checksum})
+
+        return entity
+
+    def apply_edit_operation(
+        self,
+        current_content: str,
+        operation: str,
+        content: str,
+        section: Optional[str] = None,
+        find_text: Optional[str] = None,
+        expected_replacements: int = 1,
+    ) -> str:
+        """Apply the specified edit operation to the current content."""
+
+        if operation == "append":
+            # Ensure proper spacing
+            if current_content and not current_content.endswith("\n"):
+                return current_content + "\n" + content
+            return current_content + content  # pragma: no cover
+
+        elif operation == "prepend":
+            # Handle frontmatter-aware prepending
+            return self._prepend_after_frontmatter(current_content, content)
+
+        elif operation == "find_replace":
+            if not find_text:
+                raise ValueError("find_text is required for find_replace operation")
+            if not find_text.strip():
+                raise ValueError("find_text cannot be empty or whitespace only")
+
+            # Count actual occurrences
+            actual_count = current_content.count(find_text)
+
+            # Validate count matches expected
+            if actual_count != expected_replacements:
+                if actual_count == 0:
+                    raise ValueError(f"Text to replace not found: '{find_text}'")
+                else:
+                    raise ValueError(
+                        f"Expected {expected_replacements} occurrences of '{find_text}', "
+                        f"but found {actual_count}"
+                    )
+
+            return current_content.replace(find_text, content)
+
+        elif operation == "replace_section":
+            if not section:
+                raise ValueError("section is required for replace_section operation")
+            if not section.strip():
+                raise ValueError("section cannot be empty or whitespace only")
+            return self.replace_section_content(current_content, section, content)
+
+        else:
+            raise ValueError(f"Unsupported operation: {operation}")
+
+    def replace_section_content(
+        self, current_content: str, section_header: str, new_content: str
+    ) -> str:
+        """Replace content under a specific markdown section header.
+
+        This method uses a simple, safe approach: when replacing a section, it only
+        replaces the immediate content under that header until it encounters the next
+        header of ANY level. This means:
+
+        - Replacing "# Header" replaces content until "## Subsection" (preserves subsections)
+        - Replacing "## Section" replaces content until "### Subsection" (preserves subsections)
+        - More predictable and safer than trying to consume entire hierarchies
+
+        Args:
+            current_content: The current markdown content
+            section_header: The section header to find and replace (e.g., "## Section Name")
+            new_content: The new content to replace the section with (should not include the header itself)
+
+        Returns:
+            The updated content with the section replaced
+
+        Raises:
+            ValueError: If multiple sections with the same header are found
+        """
+        # Normalize the section header (ensure it starts with #)
+        if not section_header.startswith("#"):
+            section_header = "## " + section_header
+
+        # Strip duplicate header from new_content if present (fix for issue #390)
+        # LLMs sometimes include the section header in their content, which would create duplicates
+        new_content_lines = new_content.lstrip().split("\n")
+        if new_content_lines and new_content_lines[0].strip() == section_header.strip():
+            # Remove the duplicate header line
+            new_content = "\n".join(new_content_lines[1:]).lstrip()
+
+        # First pass: count matching sections to check for duplicates
+        lines = current_content.split("\n")
+        matching_sections = []
+
+        for i, line in enumerate(lines):
+            if line.strip() == section_header.strip():
+                matching_sections.append(i)
+
+        # Handle multiple sections error
+        if len(matching_sections) > 1:
+            raise ValueError(
+                f"Multiple sections found with header '{section_header}'. "
+                f"Section replacement requires unique headers."
             )
+
+        # If no section found, append it
+        if len(matching_sections) == 0:
+            logger.info(f"Section '{section_header}' not found, appending to end of document")
+            separator = "\n\n" if current_content and not current_content.endswith("\n\n") else ""
+            return current_content + separator + section_header + "\n" + new_content
+
+        # Replace the single matching section
+        result_lines = []
+        section_line_idx = matching_sections[0]
+
+        i = 0
+        while i < len(lines):
+            line = lines[i]
+
+            # Check if this is our target section header
+            if i == section_line_idx:
+                # Add the section header and new content
+                result_lines.append(line)
+                result_lines.append(new_content)
+                i += 1
+
+                # Skip the original section content until next header or end
+                while i < len(lines):
+                    next_line = lines[i]
+                    # Stop consuming when we hit any header (preserve subsections)
+                    if next_line.startswith("#"):
+                        # We found another header - continue processing from here
+                        break
+                    i += 1
+                # Continue processing from the next header (don't increment i again)
+                continue
+
+            # Add all other lines (including subsequent sections)
+            result_lines.append(line)
+            i += 1
+
+        return "\n".join(result_lines)
+
+    def _prepend_after_frontmatter(self, current_content: str, content: str) -> str:
+        """Prepend content after frontmatter, preserving frontmatter structure."""
+
+        # Check if file has frontmatter
+        if has_frontmatter(current_content):
             try:
-                await self.relation_repository.add(relation)
-            except IntegrityError:
-                # Unique constraint violation - relation already exists
-                logger.debug(
-                    f"Skipping duplicate relation {rel.type} from {db_entity.permalink} target: {rel.target}, type: {rel.type}"
+                # Parse and separate frontmatter from body
+                frontmatter_data = parse_frontmatter(current_content)
+                body_content = remove_frontmatter(current_content)
+
+                # Prepend content to the body
+                if content and not content.endswith("\n"):
+                    new_body = content + "\n" + body_content
+                else:
+                    new_body = content + body_content
+
+                # Reconstruct file with frontmatter + prepended body
+                yaml_fm = yaml.dump(frontmatter_data, sort_keys=False, allow_unicode=True)
+                return f"---\n{yaml_fm}---\n\n{new_body.strip()}"
+
+            except Exception as e:  # pragma: no cover
+                logger.warning(
+                    f"Failed to parse frontmatter during prepend: {e}"
+                )  # pragma: no cover
+                # Fall back to simple prepend if frontmatter parsing fails  # pragma: no cover
+
+        # No frontmatter or parsing failed - do simple prepend  # pragma: no cover
+        if content and not content.endswith("\n"):  # pragma: no cover
+            return content + "\n" + current_content  # pragma: no cover
+        return content + current_content  # pragma: no cover
+
+    async def move_entity(
+        self,
+        identifier: str,
+        destination_path: str,
+        project_config: ProjectConfig,
+        app_config: BasicMemoryConfig,
+    ) -> EntityModel:
+        """Move entity to new location with database consistency.
+
+        Args:
+            identifier: Entity identifier (title, permalink, or memory:// URL)
+            destination_path: New path relative to project root
+            project_config: Project configuration for file operations
+            app_config: App configuration for permalink update settings
+
+        Returns:
+            Success message with move details
+
+        Raises:
+            EntityNotFoundError: If the entity cannot be found
+            ValueError: If move operation fails due to validation or filesystem errors
+        """
+        logger.debug(f"Moving entity: {identifier} to {destination_path}")
+
+        # 1. Resolve identifier to entity with strict mode for destructive operations
+        entity = await self.link_resolver.resolve_link(identifier, strict=True)
+        if not entity:
+            raise EntityNotFoundError(f"Entity not found: {identifier}")
+
+        current_path = entity.file_path
+        old_permalink = entity.permalink
+
+        # 2. Validate destination path format first
+        if not destination_path or destination_path.startswith("/") or not destination_path.strip():
+            raise ValueError(f"Invalid destination path: {destination_path}")
+
+        # 3. Validate paths
+        # NOTE: In tenantless/cloud mode, we cannot rely on local filesystem paths.
+        # Use FileService for existence checks and moving.
+        if not await self.file_service.exists(current_path):
+            raise ValueError(f"Source file not found: {current_path}")
+
+        if await self.file_service.exists(destination_path):
+            raise ValueError(f"Destination already exists: {destination_path}")
+
+        try:
+            # 4. Ensure destination directory if needed (no-op for S3)
+            await self.file_service.ensure_directory(Path(destination_path).parent)
+
+            # 5. Move physical file via FileService (filesystem rename or cloud move)
+            await self.file_service.move_file(current_path, destination_path)
+            logger.info(f"Moved file: {current_path} -> {destination_path}")
+
+            # 6. Prepare database updates
+            updates = {"file_path": destination_path}
+
+            # 7. Update permalink if configured or if entity has null permalink (unless disabled)
+            if not app_config.disable_permalinks and (
+                app_config.update_permalinks_on_move or old_permalink is None
+            ):
+                # Generate new permalink from destination path
+                new_permalink = await self.resolve_permalink(destination_path)
+
+                # Update frontmatter with new permalink
+                await self.file_service.update_frontmatter(
+                    destination_path, {"permalink": new_permalink}
                 )
-                continue
 
-        return await self.repository.get_by_file_path(str(file_path))
+                updates["permalink"] = new_permalink
+                if old_permalink is None:
+                    logger.info(
+                        f"Generated permalink for entity with null permalink: {new_permalink}"
+                    )
+                else:
+                    logger.info(f"Updated permalink: {old_permalink} -> {new_permalink}")
+
+            # 8. Recalculate checksum
+            new_checksum = await self.file_service.compute_checksum(destination_path)
+            updates["checksum"] = new_checksum
+
+            # 9. Update database
+            updated_entity = await self.repository.update(entity.id, updates)
+            if not updated_entity:
+                raise ValueError(f"Failed to update entity in database: {entity.id}")
+
+            return updated_entity
+
+        except Exception as e:
+            # Rollback: try to restore original file location if move succeeded
+            try:
+                if await self.file_service.exists(
+                    destination_path
+                ) and not await self.file_service.exists(current_path):
+                    await self.file_service.move_file(destination_path, current_path)
+                    logger.info(f"Rolled back file move: {destination_path} -> {current_path}")
+            except Exception as rollback_error:  # pragma: no cover
+                logger.error(f"Failed to rollback file move: {rollback_error}")
+
+            # Re-raise the original error with context
+            raise ValueError(f"Move failed: {str(e)}") from e