[BUG] BM loses track of note after editing it with vim

[discapes]

When I create a note in BM, edit it with vim (don't have to even change anything), BM cannot find it anymore. Running bm sync fixes this, but it isn't synced automatically.

Steps To Reproduce

bm tool write-note --title test --folder '' --content 'hello'
bm tool read-note test # works
vim test.md # don't change anything, just :wq
bm tool read-note test # doesn't find the note

Environment

• OS: Debian GNU/Linux 12 (bookworm) podman container inside NixOS 25.05 (Warbler)
• Python version: Python 3.11.2
• Basic Memory version: 0.14.3
• Installation method: uv

Output:

root@fbadba956d98:~/basic-memory# bm tool write-note --title test --folder '' --content 'hello'
2025-08-07 15:23:00.906 | INFO     | basic_memory.utils:setup_logging:167 - ENV: 'dev' Log level: 'INFO' Logging to .basic-memory/basic-memory-api.log
2025-08-07 15:23:00.906 | INFO     | basic_memory.config:setup_basic_memory_logging:367 - Basic Memory 0.14.3 (Project: main)
2025-08-07 15:23:02.196 | DEBUG    | basic_memory.api.template_loader:__init__:235 - Initialized template loader with directory: /root/.local/share/uv/tools/basic-memory/lib/python3.12/site-packages/basic_memory/templates
2025-08-07 15:23:02.319 | DEBUG    | basic_memory.mcp.async_client:create_client:23 - Creating ASGI client for local Basic Memory API
2025-08-07 15:23:02.361 | INFO     | basic_memory.services.initialization:initialize_app:156 - Initializing app...
2025-08-07 15:23:02.362 | DEBUG    | basic_memory.db:_create_engine_and_session:81 - Creating engine for db_url: sqlite+aiosqlite:////root/.basic-memory/memory.db
2025-08-07 15:23:02.365 | INFO     | basic_memory.db:run_migrations:176 - Running database migrations...
2025-08-07 15:23:02.370 | INFO     | basic_memory.db:run_migrations:195 - Migrations completed successfully
2025-08-07 15:23:02.370 | INFO     | basic_memory.repository.search_repository:init_search_index:115 - Initializing search index
2025-08-07 15:23:02.373 | INFO     | basic_memory.services.initialization:initialize_database:30 - Database initialization completed
2025-08-07 15:23:02.373 | INFO     | basic_memory.services.initialization:reconcile_projects_with_config:47 - Reconciling projects from config with database...
2025-08-07 15:23:02.373 | INFO     | basic_memory.services.project_service:synchronize_projects:233 - Synchronizing projects between database and configuration
2025-08-07 15:23:02.383 | DEBUG    | basic_memory.repository.repository:find_all:157 - Finding all Project (skip=0, limit=None)
2025-08-07 15:23:02.384 | DEBUG    | basic_memory.repository.repository:find_all:170 - Found 1 Project records
2025-08-07 15:23:02.386 | INFO     | basic_memory.services.project_service:synchronize_projects:301 - Project synchronization complete
2025-08-07 15:23:02.387 | INFO     | basic_memory.mcp.project_session:initialize:34 - Initialized project session with default project: main
2025-08-07 15:23:02.387 | INFO     | basic_memory.mcp.project_session:refresh_from_config:81 - Refreshed project session from config, new default: main
2025-08-07 15:23:02.387 | INFO     | basic_memory.services.initialization:reconcile_projects_with_config:64 - Projects successfully reconciled between config and database
2025-08-07 15:23:02.387 | INFO     | basic_memory.services.initialization:initialize_app:163 - App initialization completed (migration running in background if needed)
2025-08-07 15:23:02.387 | INFO     | basic_memory.services.initialization:ensure_initialization:177 - Initialization completed successfully: result=None
2025-08-07 15:23:02.387 | INFO     | basic_memory.mcp.project_session:set_current_project:53 - Switched project context: main -> main
2025-08-07 15:23:02.388 | INFO     | basic_memory.mcp.tools.write_note:write_note:73 - MCP tool call tool=write_note folder=, title=test, tags=None
2025-08-07 15:23:02.389 | DEBUG    | basic_memory.mcp.tools.write_note:write_note:110 - Creating entity via API permalink=test
2025-08-07 15:23:02.389 | DEBUG    | basic_memory.mcp.tools.utils:call_put:192 - Calling PUT '/main/knowledge/entities/test'
2025-08-07 15:23:02.396 | DEBUG    | basic_memory.deps:get_file_service:230 - Creating FileService for project: main, base_path: /root/basic-memory
2025-08-07 15:23:02.396 | DEBUG    | basic_memory.deps:get_file_service:234 - Created FileService for project: <basic_memory.services.file_service.FileService object at 0x7fe319d292b0> 
2025-08-07 15:23:02.400 | INFO     | basic_memory.api.routers.knowledge_router:create_or_update_entity:70 - API request: create_or_update_entity for project='main', permalink='test', data.entity_type='note', data.title='test'
2025-08-07 15:23:02.400 | DEBUG    | basic_memory.services.entity_service:create_or_update_entity:138 - Creating or updating entity: test.md, permalink: test
2025-08-07 15:23:02.418 | DEBUG    | basic_memory.services.entity_service:create_entity:156 - Creating entity: test
2025-08-07 15:23:02.418 | DEBUG    | basic_memory.services.file_service:exists:98 - Checking file existence: path=test.md
2025-08-07 15:23:02.418 | DEBUG    | basic_memory.repository.repository:find_all:157 - Finding all Entity (skip=0, limit=None)
2025-08-07 15:23:02.425 | DEBUG    | basic_memory.repository.repository:find_all:170 - Found 4 Entity records
2025-08-07 15:23:02.429 | INFO     | basic_memory.services.file_service:write_file:132 - Writing file: path=test.md, content_length=53, is_markdown=True
2025-08-07 15:23:02.430 | DEBUG    | basic_memory.file_utils:write_file_atomic:90 - Wrote file atomically
2025-08-07 15:23:02.430 | DEBUG    | basic_memory.services.file_service:write_file:143 - File write completed path=/root/basic-memory/test.md, checksum='b1ff04050bd6ed37e18cb6204b1e58b57ac07c295ad325d090406ff5e22b0bbe'
2025-08-07 15:23:02.430 | DEBUG    | basic_memory.services.entity_service:create_entity_from_markdown:354 - Creating entity: test file_path: test.md
2025-08-07 15:23:02.441 | DEBUG    | basic_memory.services.entity_service:update_entity_relations:413 - Updating relations for entity: test.md
2025-08-07 15:23:02.453 | DEBUG    | basic_memory.repository.repository:update:258 - Updating Entity 5 with data: {'checksum': 'b1ff04050bd6ed37e18cb6204b1e58b57ac07c295ad325d090406ff5e22b0bbe'}
2025-08-07 15:23:02.457 | DEBUG    | basic_memory.repository.repository:update:278 - Updated Entity: 5
2025-08-07 15:23:02.465 | INFO     | basic_memory.sync.sync_service:resolve_relations:556 - Resolving forward references
2025-08-07 15:23:02.465 | DEBUG    | basic_memory.api.routers.knowledge_router:create_or_update_entity:96 - Resolved relations after creating entity: test
2025-08-07 15:23:02.465 | INFO     | basic_memory.api.routers.knowledge_router:create_or_update_entity:103 - API response: result.title='test', result.permalink='test', created=True, status_code=201
2025-08-07 15:23:02.467 | DEBUG    | basic_memory.services.file_service:read_entity_content:63 - Reading entity content, entity_id=5, permalink=test
/root/.local/share/uv/tools/basic-memory/lib/python3.12/site-packages/aiosqlite/core.py:105: DeprecationWarning: The default datetime adapter is deprecated as of Python 3.12; see the sqlite3 documentation for suggested replacement recipes
  result = function()
2025-08-07 15:23:02.469 | DEBUG    | basic_memory.repository.search_repository:index_item:553 - indexed row SearchIndexRow(project_id=1, id=5, type='entity', file_path='test.md', created_at=datetime.datetime(2025, 8, 7, 15, 23, 2, 429642), updated_at=datetime.datetime(2025, 8, 7, 15, 23, 2, 429642), permalink='test', metadata={'entity_type': 'note'}, score=None, title='test', content_stems='tes\ntest\nest\nhello\ntes\ntest\nest\nst.\ntest.md\ntes\n.md\nest\nt.m', content_snippet='hello', entity_id=5, category=None, from_id=None, to_id=None, relation_type=None)
2025-08-07 15:23:02.473 | INFO     | basic_memory.mcp.tools.write_note:write_note:154 - MCP tool response: tool=write_note action=Created permalink=test observations_count=0 relations_count=0 resolved_relations=0 unresolved_relations=0 status_code=201
# Created note
file_path: test.md
permalink: test
checksum: b1ff0405
root@fbadba956d98:~/basic-memory# bm tool read-note test
2025-08-07 15:23:21.967 | INFO     | basic_memory.utils:setup_logging:167 - ENV: 'dev' Log level: 'INFO' Logging to .basic-memory/basic-memory-api.log
2025-08-07 15:23:21.968 | INFO     | basic_memory.config:setup_basic_memory_logging:367 - Basic Memory 0.14.3 (Project: main)
2025-08-07 15:23:23.295 | DEBUG    | basic_memory.api.template_loader:__init__:235 - Initialized template loader with directory: /root/.local/share/uv/tools/basic-memory/lib/python3.12/site-packages/basic_memory/templates
2025-08-07 15:23:23.428 | DEBUG    | basic_memory.mcp.async_client:create_client:23 - Creating ASGI client for local Basic Memory API
2025-08-07 15:23:23.473 | INFO     | basic_memory.services.initialization:initialize_app:156 - Initializing app...
2025-08-07 15:23:23.473 | DEBUG    | basic_memory.db:_create_engine_and_session:81 - Creating engine for db_url: sqlite+aiosqlite:////root/.basic-memory/memory.db
2025-08-07 15:23:23.476 | INFO     | basic_memory.db:run_migrations:176 - Running database migrations...
2025-08-07 15:23:23.481 | INFO     | basic_memory.db:run_migrations:195 - Migrations completed successfully
2025-08-07 15:23:23.481 | INFO     | basic_memory.repository.search_repository:init_search_index:115 - Initializing search index
2025-08-07 15:23:23.484 | INFO     | basic_memory.services.initialization:initialize_database:30 - Database initialization completed
2025-08-07 15:23:23.484 | INFO     | basic_memory.services.initialization:reconcile_projects_with_config:47 - Reconciling projects from config with database...
2025-08-07 15:23:23.484 | INFO     | basic_memory.services.project_service:synchronize_projects:233 - Synchronizing projects between database and configuration
2025-08-07 15:23:23.494 | DEBUG    | basic_memory.repository.repository:find_all:157 - Finding all Project (skip=0, limit=None)
2025-08-07 15:23:23.495 | DEBUG    | basic_memory.repository.repository:find_all:170 - Found 1 Project records
2025-08-07 15:23:23.497 | INFO     | basic_memory.services.project_service:synchronize_projects:301 - Project synchronization complete
2025-08-07 15:23:23.498 | INFO     | basic_memory.mcp.project_session:initialize:34 - Initialized project session with default project: main
2025-08-07 15:23:23.498 | INFO     | basic_memory.mcp.project_session:refresh_from_config:81 - Refreshed project session from config, new default: main
2025-08-07 15:23:23.498 | INFO     | basic_memory.services.initialization:reconcile_projects_with_config:64 - Projects successfully reconciled between config and database
2025-08-07 15:23:23.498 | INFO     | basic_memory.services.initialization:initialize_app:163 - App initialization completed (migration running in background if needed)
2025-08-07 15:23:23.499 | INFO     | basic_memory.services.initialization:ensure_initialization:177 - Initialization completed successfully: result=None
2025-08-07 15:23:23.499 | INFO     | basic_memory.mcp.project_session:set_current_project:53 - Switched project context: main -> main
2025-08-07 15:23:23.500 | INFO     | basic_memory.mcp.tools.read_note:read_note:83 - Attempting to read note from URL: /main/resource/test
2025-08-07 15:23:23.500 | DEBUG    | basic_memory.mcp.tools.utils:call_get:108 - Calling GET '/main/resource/test' params: '{'page': 1, 'page_size': 10}'
2025-08-07 15:23:23.508 | DEBUG    | basic_memory.deps:get_file_service:230 - Creating FileService for project: main, base_path: /root/basic-memory
2025-08-07 15:23:23.508 | DEBUG    | basic_memory.deps:get_file_service:234 - Created FileService for project: <basic_memory.services.file_service.FileService object at 0x7f1f4d641310> 
2025-08-07 15:23:23.509 | DEBUG    | basic_memory.api.routers.resource_router:get_resource_content:55 - Getting content for: test
2025-08-07 15:23:23.518 | DEBUG    | basic_memory.services.link_resolver:resolve_link:47 - Found exact permalink match: test
2025-08-07 15:23:23.521 | INFO     | basic_memory.mcp.tools.read_note:read_note:91 - Returning read_note result from resource: test
---
title: test
type: note
permalink: test
---

hello
root@fbadba956d98:~/basic-memory# vim test.md 
root@fbadba956d98:~/basic-memory# bm tool read-note test
2025-08-07 15:23:35.185 | INFO     | basic_memory.utils:setup_logging:167 - ENV: 'dev' Log level: 'INFO' Logging to .basic-memory/basic-memory-api.log
2025-08-07 15:23:35.185 | INFO     | basic_memory.config:setup_basic_memory_logging:367 - Basic Memory 0.14.3 (Project: main)
2025-08-07 15:23:36.480 | DEBUG    | basic_memory.api.template_loader:__init__:235 - Initialized template loader with directory: /root/.local/share/uv/tools/basic-memory/lib/python3.12/site-packages/basic_memory/templates
2025-08-07 15:23:36.607 | DEBUG    | basic_memory.mcp.async_client:create_client:23 - Creating ASGI client for local Basic Memory API
2025-08-07 15:23:36.653 | INFO     | basic_memory.services.initialization:initialize_app:156 - Initializing app...
2025-08-07 15:23:36.653 | DEBUG    | basic_memory.db:_create_engine_and_session:81 - Creating engine for db_url: sqlite+aiosqlite:////root/.basic-memory/memory.db
2025-08-07 15:23:36.657 | INFO     | basic_memory.db:run_migrations:176 - Running database migrations...
2025-08-07 15:23:36.664 | INFO     | basic_memory.db:run_migrations:195 - Migrations completed successfully
2025-08-07 15:23:36.664 | INFO     | basic_memory.repository.search_repository:init_search_index:115 - Initializing search index
2025-08-07 15:23:36.667 | INFO     | basic_memory.services.initialization:initialize_database:30 - Database initialization completed
2025-08-07 15:23:36.667 | INFO     | basic_memory.services.initialization:reconcile_projects_with_config:47 - Reconciling projects from config with database...
2025-08-07 15:23:36.667 | INFO     | basic_memory.services.project_service:synchronize_projects:233 - Synchronizing projects between database and configuration
2025-08-07 15:23:36.677 | DEBUG    | basic_memory.repository.repository:find_all:157 - Finding all Project (skip=0, limit=None)
2025-08-07 15:23:36.679 | DEBUG    | basic_memory.repository.repository:find_all:170 - Found 1 Project records
2025-08-07 15:23:36.681 | INFO     | basic_memory.services.project_service:synchronize_projects:301 - Project synchronization complete
2025-08-07 15:23:36.681 | INFO     | basic_memory.mcp.project_session:initialize:34 - Initialized project session with default project: main
2025-08-07 15:23:36.682 | INFO     | basic_memory.mcp.project_session:refresh_from_config:81 - Refreshed project session from config, new default: main
2025-08-07 15:23:36.682 | INFO     | basic_memory.services.initialization:reconcile_projects_with_config:64 - Projects successfully reconciled between config and database
2025-08-07 15:23:36.682 | INFO     | basic_memory.services.initialization:initialize_app:163 - App initialization completed (migration running in background if needed)
2025-08-07 15:23:36.682 | INFO     | basic_memory.services.initialization:ensure_initialization:177 - Initialization completed successfully: result=None
2025-08-07 15:23:36.682 | INFO     | basic_memory.mcp.project_session:set_current_project:53 - Switched project context: main -> main
2025-08-07 15:23:36.684 | INFO     | basic_memory.mcp.tools.read_note:read_note:83 - Attempting to read note from URL: /main/resource/test
2025-08-07 15:23:36.684 | DEBUG    | basic_memory.mcp.tools.utils:call_get:108 - Calling GET '/main/resource/test' params: '{'page': 1, 'page_size': 10}'
2025-08-07 15:23:36.692 | DEBUG    | basic_memory.deps:get_file_service:230 - Creating FileService for project: main, base_path: /root/basic-memory
2025-08-07 15:23:36.692 | DEBUG    | basic_memory.deps:get_file_service:234 - Created FileService for project: <basic_memory.services.file_service.FileService object at 0x7f008bc8fec0> 
2025-08-07 15:23:36.693 | DEBUG    | basic_memory.api.routers.resource_router:get_resource_content:55 - Getting content for: test
2025-08-07 15:23:36.706 | INFO     | basic_memory.mcp.tools.utils:call_get:140 - Client error: GET /main/resource/test: Resource not found: test
2025-08-07 15:23:36.707 | INFO     | basic_memory.mcp.tools.read_note:read_note:94 - Direct lookup failed for '/main/resource/test': Resource not found: test
2025-08-07 15:23:36.707 | INFO     | basic_memory.mcp.tools.read_note:read_note:98 - Search title for: test
2025-08-07 15:23:36.707 | INFO     | basic_memory.mcp.tools.search:search_notes:349 - Searching for permalink=None permalink_match=None text=None title='test' types=None entity_types=None after_date=None
2025-08-07 15:23:36.707 | DEBUG    | basic_memory.mcp.tools.utils:call_post:385 - Calling POST '/main/search/'
2025-08-07 15:23:36.713 | DEBUG    | basic_memory.deps:get_file_service:230 - Creating FileService for project: main, base_path: /root/basic-memory
2025-08-07 15:23:36.714 | DEBUG    | basic_memory.deps:get_file_service:234 - Created FileService for project: <basic_memory.services.file_service.FileService object at 0x7f009041dd90> 
2025-08-07 15:23:36.717 | DEBUG    | basic_memory.mcp.tools.utils:call_post:402 - response: {'results': [], 'current_page': 1, 'page_size': 10}
2025-08-07 15:23:36.718 | INFO     | basic_memory.mcp.tools.search:search_notes:362 - Search returned no results for query: test
2025-08-07 15:23:36.718 | INFO     | basic_memory.mcp.tools.read_note:read_note:119 - No results in title search for: test
2025-08-07 15:23:36.718 | INFO     | basic_memory.mcp.tools.read_note:read_note:122 - Title search failed, trying text search for: test
2025-08-07 15:23:36.719 | INFO     | basic_memory.mcp.tools.search:search_notes:349 - Searching for permalink=None permalink_match=None text='test' title=None types=None entity_types=None after_date=None
2025-08-07 15:23:36.719 | DEBUG    | basic_memory.mcp.tools.utils:call_post:385 - Calling POST '/main/search/'
2025-08-07 15:23:36.724 | DEBUG    | basic_memory.deps:get_file_service:230 - Creating FileService for project: main, base_path: /root/basic-memory
2025-08-07 15:23:36.724 | DEBUG    | basic_memory.deps:get_file_service:234 - Created FileService for project: <basic_memory.services.file_service.FileService object at 0x7f009029a690> 
2025-08-07 15:23:36.726 | DEBUG    | basic_memory.mcp.tools.utils:call_post:402 - response: {'results': [], 'current_page': 1, 'page_size': 10}
2025-08-07 15:23:36.726 | INFO     | basic_memory.mcp.tools.search:search_notes:362 - Search returned no results for query: test

# Note Not Found: "test"

I searched for "test" using multiple methods (direct lookup, title search, and text search) but couldn't find any matching notes. Here are some suggestions:
....

[discapes]

This is what bm status shows, I can run it multiple times without anything happening.

root@fbadba956d98:~/basic-memory# bm status
2025-08-07 15:29:23.029 | INFO     | basic_memory.utils:setup_logging:167 - ENV: 'dev' Log level: 'INFO' Logging to .basic-memory/basic-memory-api.log
2025-08-07 15:29:23.030 | INFO     | basic_memory.config:setup_basic_memory_logging:367 - Basic Memory 0.14.3 (Project: main)
2025-08-07 15:29:24.285 | DEBUG    | basic_memory.api.template_loader:__init__:235 - Initialized template loader with directory: /root/.local/share/uv/tools/basic-memory/lib/python3.12/site-packages/basic_memory/templates
2025-08-07 15:29:24.408 | DEBUG    | basic_memory.mcp.async_client:create_client:23 - Creating ASGI client for local Basic Memory API
2025-08-07 15:29:24.450 | INFO     | basic_memory.services.initialization:initialize_app:156 - Initializing app...
2025-08-07 15:29:24.451 | DEBUG    | basic_memory.db:_create_engine_and_session:81 - Creating engine for db_url: sqlite+aiosqlite:////root/.basic-memory/memory.db
2025-08-07 15:29:24.454 | INFO     | basic_memory.db:run_migrations:176 - Running database migrations...
2025-08-07 15:29:24.459 | INFO     | basic_memory.db:run_migrations:195 - Migrations completed successfully
2025-08-07 15:29:24.459 | INFO     | basic_memory.repository.search_repository:init_search_index:115 - Initializing search index
2025-08-07 15:29:24.462 | INFO     | basic_memory.services.initialization:initialize_database:30 - Database initialization completed
2025-08-07 15:29:24.462 | INFO     | basic_memory.services.initialization:reconcile_projects_with_config:47 - Reconciling projects from config with database...
2025-08-07 15:29:24.463 | INFO     | basic_memory.services.project_service:synchronize_projects:233 - Synchronizing projects between database and configuration
2025-08-07 15:29:24.472 | DEBUG    | basic_memory.repository.repository:find_all:157 - Finding all Project (skip=0, limit=None)
2025-08-07 15:29:24.473 | DEBUG    | basic_memory.repository.repository:find_all:170 - Found 1 Project records
2025-08-07 15:29:24.475 | INFO     | basic_memory.services.project_service:synchronize_projects:301 - Project synchronization complete
2025-08-07 15:29:24.476 | INFO     | basic_memory.mcp.project_session:initialize:34 - Initialized project session with default project: main
2025-08-07 15:29:24.476 | INFO     | basic_memory.mcp.project_session:refresh_from_config:81 - Refreshed project session from config, new default: main
2025-08-07 15:29:24.476 | INFO     | basic_memory.services.initialization:reconcile_projects_with_config:64 - Projects successfully reconciled between config and database
2025-08-07 15:29:24.476 | INFO     | basic_memory.services.initialization:initialize_app:163 - App initialization completed (migration running in background if needed)
2025-08-07 15:29:24.476 | INFO     | basic_memory.services.initialization:ensure_initialization:177 - Initialization completed successfully: result=None
2025-08-07 15:29:24.476 | INFO     | basic_memory.mcp.project_session:set_current_project:53 - Switched project context: main -> main
2025-08-07 15:29:24.480 | DEBUG    | basic_memory.repository.repository:find_all:157 - Finding all Entity (skip=0, limit=None)
2025-08-07 15:29:24.489 | DEBUG    | basic_memory.repository.repository:find_all:170 - Found 4 Entity records
2025-08-07 15:29:24.490 | INFO     | basic_memory.sync.sync_service:get_db_file_state:241 - Found 4 db records
2025-08-07 15:29:24.490 | INFO     | basic_memory.sync.sync_service:scan:189 - Scanning directory /root/basic-memory. Found 4 db paths
2025-08-07 15:29:24.490 | DEBUG    | basic_memory.sync.sync_service:scan_directory:609 - Scanning directory /root/basic-memory
2025-08-07 15:29:24.492 | DEBUG    | basic_memory.sync.sync_service:scan_directory:630 - /root/basic-memory scan completed directory=/root/basic-memory files_found=5 duration_ms=2
2025-08-07 15:29:24.492 | INFO     | basic_memory.sync.sync_service:scan:229 - Completed scan for directory /root/basic-memory, found 1 changes.
╭─────────────────────╮
│ main: Status        │
│ └── test.md/ +1 new │
╰─────────────────────╯

[discapes]

And I find this in the log after editing the file

2025-08-07 15:31:16.531 | INFO     | basic_memory.sync.watch_service:handle_changes:189 - Processing project: main changes, change_count=6, directory=/root/basic-memory
2025-08-07 15:31:16.547 | INFO     | basic_memory.sync.sync_service:handle_delete:426 - Deleting entity with file_path=test.md, entity_id=5, permalink=test
2025-08-07 15:31:16.557 | INFO     | basic_memory.sync.watch_service:handle_changes:291 - deleted: test.md
2025-08-07 15:31:16.557 | INFO     | basic_memory.sync.watch_service:handle_changes:384 - changes: 2
2025-08-07 15:31:16.557 | INFO     | basic_memory.sync.watch_service:handle_changes:390 - File change processing completed, processed_files=3, total_synced_files=13, duration_ms=26

[discapes]

root@fbadba956d98:/# inotifywait -m -c root/basic-memory/test.md 
Setting up watches.
Watches established.
root/basic-memory/test.md,OPEN,
root/basic-memory/test.md,"CLOSE_NOWRITE,CLOSE",
root/basic-memory/test.md,OPEN,
root/basic-memory/test.md,ACCESS,
root/basic-memory/test.md,"CLOSE_NOWRITE,CLOSE",
root/basic-memory/test.md,MOVE_SELF,
root/basic-memory/test.md,ATTRIB,
root/basic-memory/test.md,DELETE_SELF,

perhaps related to https://vi.stackexchange.com/questions/32973/how-can-i-stop-vim-from-moving-deleting-a-file-just-before-saving

[discapes]

When I use :set backupcopy=yes with Vim, I can edit the note without issues. But I think the default behaviour of vim is something that should maybe be accounted for in bm's watch function, even if it can be worked around.

[phernandez]

Oh, yes, vim is being too clever, I think. BM also watches for file notifications. If it sees a delete it will remove the file from the index. It should add it again when it finds the new one. But if you can tell vim not to do that, it may be helpful.

@claude if the file is deleted because vim is doing an atomic file write via a swap file, why is the new version not being picked up?

[claude]

Claude finished @phernandez's task —— View job

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Analysis Complete: Vim Atomic Write Issue

• Read file watching service code to understand file change detection
• Examine sync service to understand how deletions are handled
• Analyze why new file creation after atomic write isn't detected
• Provide technical explanation of the issue

Root Cause Analysis

The issue occurs because of vim's atomic write behavior combined with a gap in Basic Memory's file watching logic. Here's what happens:

Vim's Atomic Write Process

When vim saves a file, it performs an atomic write operation:

1. Creates a backup/swap file
2. Moves the original file out of the way (MOVE_SELF)
3. Writes new content to the original filename
4. Sets file attributes (ATTRIB)
5. Deletes the original file inode (DELETE_SELF)

From the inotify events you captured:

root/basic-memory/test.md,MOVE_SELF,
root/basic-memory/test.md,ATTRIB,
root/basic-memory/test.md,DELETE_SELF,

Basic Memory's Handling

The watch service in src/basic_memory/sync/watch_service.py correctly detects these events but processes them in this order:

1. DELETE_SELF is detected first → triggers handle_delete() which removes the entity from the database and search index
2. The new file creation should trigger an ADD event → but this isn't happening reliably

The Problem: Missing ADD Detection

Looking at the code in watch_service.py:145-162, the filter_changes() method should allow the new file to be detected:

def filter_changes(self, change: Change, path: str) -> bool:
    # Skip hidden directories and files
    path_parts = Path(path).parts
    for part in path_parts:
        if part.startswith("."):
            return False
    
    # Skip temp files used in atomic operations  
    if path.endswith(".tmp"):
        return False
    
    return True

The issue appears to be that vim's atomic write sequence generates a DELETE_SELF event but may not generate a corresponding ADD event for the new file with the same name, since from the filesystem's perspective, the filename never disappeared - only the inode changed.

Why Manual Sync Works

The scan_directory() method in sync_service.py:597-637 uses os.walk() to discover all files in the directory, regardless of watch events. This is why bm sync finds and re-indexes the file.

The Fix Location

The issue could be addressed in watch_service.py:217-224 where there's already logic to handle atomic writes:

# because of our atomic writes on updates, an add may be an existing file
for added_path in adds:  # pragma: no cover TODO add test
    entity = await sync_service.entity_repository.get_by_file_path(added_path)
    if entity is not None:
        logger.debug(f"Existing file will be processed as modified, path={added_path}")
        adds.remove(added_path)
        modifies.append(added_path)

However, the problem is that no ADD event is being generated for vim's atomic writes, so this code never runs.

The solution would be to detect when a DELETE event occurs for a file that still exists on disk, and treat it as a modification rather than a true deletion.

---

[phernandez]

@claude make a PR for the DELETE with out ADD vim special case. And be sure to add tests. This will be a special case, but keep the code clean. If it turns into a mess, stop and state what the problem is and we will revisit it.

[claude]

Claude finished @phernandez's task —— View job • claude/issue-248-20250807-1922 • Create PR ➔

---

Fix Vim Atomic Write Issue ✅

Successfully implemented fix for DELETE without ADD vim special case where vim's atomic write operations cause Basic Memory to lose track of files.

Todo List

• Read and understand current watch service and sync service logic
• Identify optimal location for the DELETE + file exists = modification fix
• Implement the special case handling for vim atomic writes
• Add comprehensive tests for the vim atomic write scenario
• Run existing tests to ensure no regressions (requires user to run - env not available)
• Commit and push changes with proper co-authored attribution
• Create PR with detailed description

Implementation Details

Fix Applied: Modified watch_service.py:284-306 in the handle_changes() method to detect when a DELETE event occurs but the file still exists on disk. This handles vim's atomic write pattern where:

1. Vim generates a DELETE_SELF inotify event when replacing the file inode
2. No corresponding ADD event is generated since the filename never disappeared
3. The file still exists on disk with new content

Key Changes:

• Check if file exists on disk before processing DELETE event
• If file exists despite DELETE event, treat as modification (call sync_file(new=False))
• Log as "atomic write detected" and display as "✎ filename (atomic write)"
• Maintain all existing delete logic for true deletions

Tests Added (4 comprehensive test cases):

1. test_handle_vim_atomic_write_delete_still_exists - Core atomic write scenario
2. test_handle_true_deletion_vs_vim_atomic - Ensures true deletions still work
3. test_handle_vim_atomic_write_markdown_with_relations - Tests with complex markdown relations
4. test_handle_vim_atomic_write_directory_path_ignored - Ensures directories are properly ignored

The code is clean, follows existing patterns, and maintains backward compatibility while fixing the vim edge case.