fix: run migrations and sync when starting mcp

docs/CLI Reference.md

@@ -29,6 +29,22 @@ Options:
 - `--watch`: Continuously monitor for changes
 - `--verbose`: Show detailed output
 
+**Note**:
+
+As of the v0.12.0 release syncing will occur in real time when the mcp process starts.
+- The real time sync means that it is no longer necessary to run the `basic-memory sync --watch` process in a a terminal to sync changes to the db (so the AI can see them). This will be done automatically.
+
+This behavior can be changed via the config. The config file for Basic Memory is in the home directory under `.basic-memory/config.json`.
+
+To change the properties, set the following values:
+```
+ ~/.basic-memory/config.json 
+{
+  "sync_changes": false,
+}
+```
+
+Thanks for using Basic Memory!
 ### import
 
 Imports external knowledge sources:

docs/Getting Started with Basic Memory.md

@@ -89,22 +89,11 @@ Replace `/absolute/path/to/uvx` with the actual path you found in Step 1.
 
 Close and reopen Claude Desktop for the changes to take effect.
 
-### 3. Start the Sync Service
+### 3. Sync changes in real time
 
-> Note the sync service is optional. You can run it if you want your local change to be available in Claude Desktop
-
-Start the sync service to monitor your files for changes:
-
-```bash
-# One-time sync
-basic-memory sync
-
-# For continuous monitoring (recommended)
-basic-memory sync --watch
-```
-
-The `--watch` flag enables automatic detection of file changes, updating your knowledge in real time.
+> **Note**: The service will sync changes from your project directory in real time so they available for the AI assistant. 
 
+To disable realtime sync, you can update the config. See [[CLI Reference#sync]].
 ### 4. Staying Updated
 
 To update Basic Memory when new versions are released:
@@ -145,8 +134,8 @@ If Claude cannot find Basic Memory tools:
 1. **Check absolute paths**: Ensure you're using complete absolute paths to uvx in the Claude Desktop configuration
 2. **Verify installation**: Run `basic-memory --version` in Terminal to confirm Basic Memory is installed
 3. **Restart applications**: Restart both Terminal and Claude Desktop after making configuration changes
-4. **Check sync status**: Ensure `basic-memory sync --watch` is running
-
+4. **Check sync status**: You can view the sync status by running `basic-memory status
+.
 #### Permission Issues
 
 If you encounter permission errors:
@@ -282,15 +271,15 @@ basic-memory import claude conversations
 basic-memory import chatgpt
 ```
 
-After importing, run `basic-memory sync` to index everything.
+After importing, the changes will be synced. Initial syncs may take a few moments. You can see info about your project by running `basic-memrory project info`.
 
 ## Quick Tips
 
-- Keep `basic-memory sync --watch` running in a terminal window
+- Basic Memory will sync changes from your project in real time.
 - Use special prompts (Continue Conversation, Recent Activity, Search) to start contextual discussions
 - Build connections between notes for a richer knowledge graph
-- Use direct memory:// URLs when you need precise context
-- Use git to version control your knowledge base
+- Use direct `memory://` URLs with a permalink when you need precise context. See [[User Guide#Using memory // URLs]]
+- Use git to version control your knowledge base (git integration is on the roadmap)
 - Review and edit AI-generated notes for accuracy
 
 ## Next Steps

docs/Knowledge Format.md

@@ -144,7 +144,19 @@ permalink: auth-approaches-2024
 ---
 ```
 
-If not specified, one will be generated automatically from the title.
+If not specified, one will be generated automatically from the title, if the note has has a frontmatter section. 
+
+By default a  notes' permalink value will not change if the file is moved. It's a **stable** identifier :). But if you'd rather permalinks are always updated when a file moves, you can set the config setting in the global config. 
+
+The config file for Basic Memory is in the home directory under `.basic-memory/config.json`.
+
+To change the behavior, set the following value:
+```
+ ~/.basic-memory/config.json 
+{
+  "update_permalinks_on_move": true
+}
+```
 
 ### Using memory:// URLs
 

src/basic_memory/api/app.py

@@ -1,6 +1,5 @@
 """FastAPI application for basic-memory knowledge graph API."""
 
-import asyncio
 from contextlib import asynccontextmanager
 
 from fastapi import FastAPI, HTTPException
@@ -10,44 +9,14 @@
 from basic_memory import db
 from basic_memory.api.routers import knowledge, memory, project_info, resource, search
 from basic_memory.config import config as project_config
-from basic_memory.config import config_manager
-from basic_memory.sync import SyncService, WatchService
-
-
-async def run_background_sync(sync_service: SyncService, watch_service: WatchService): # pragma: no cover
-    logger.info(f"Starting watch service to sync file changes in dir: {project_config.home}")
-    # full sync
-    await sync_service.sync(project_config.home, show_progress=False)
-
-    # watch changes
-    await watch_service.run()
+from basic_memory.services.initialization import initialize_app
 
 
 @asynccontextmanager
 async def lifespan(app: FastAPI):  # pragma: no cover
     """Lifecycle manager for the FastAPI app."""
-    await db.run_migrations(project_config)
-
-    # app config
-    basic_memory_config = config_manager.load_config()
-    logger.info(f"Sync changes enabled: {basic_memory_config.sync_changes}")
-    logger.info(f"Update permalinks on move enabled: {basic_memory_config.update_permalinks_on_move}")
-
-    watch_task = None
-    if basic_memory_config.sync_changes:
-        # import after migrations have run
-        from basic_memory.cli.commands.sync import get_sync_service
-
-        sync_service = await get_sync_service()
-        watch_service = WatchService(
-            sync_service=sync_service,
-            file_service=sync_service.entity_service.file_service,
-            config=project_config,
-        )
-        watch_task = asyncio.create_task(run_background_sync(sync_service, watch_service))
-    else:
-        logger.info("Sync changes disabled. Skipping watch service.")
-
+    # Initialize database and file sync services
+    watch_task = await initialize_app(project_config)
 
     # proceed with startup
     yield

src/basic_memory/cli/app.py

@@ -7,8 +7,11 @@ def version_callback(value: bool) -> None:
     """Show version and exit."""
     if value:  # pragma: no cover
         import basic_memory
+        from basic_memory.config import config
 
         typer.echo(f"Basic Memory version: {basic_memory.__version__}")
+        typer.echo(f"Current project: {config.project}")
+        typer.echo(f"Project path: {config.home}")
         raise typer.Exit()
 
 
@@ -17,11 +20,12 @@ def version_callback(value: bool) -> None:
 
 @app.callback()
 def app_callback(
+    ctx: typer.Context,
     project: Optional[str] = typer.Option(
         None,
         "--project",
         "-p",
-        help="Specify which project to use",
+        help="Specify which project to use 1",
         envvar="BASIC_MEMORY_PROJECT",
     ),
     version: Optional[bool] = typer.Option(
@@ -34,6 +38,7 @@ def app_callback(
     ),
 ) -> None:
     """Basic Memory - Local-first personal knowledge management."""
+
     # We use the project option to set the BASIC_MEMORY_PROJECT environment variable
     # The config module will pick this up when loading
     if project:  # pragma: no cover
@@ -53,6 +58,13 @@ def app_callback(
 
         config = new_config
 
+    # Run migrations for every command unless --version was specified
+    if not version and ctx.invoked_subcommand is not None:
+        from basic_memory.config import config
+        from basic_memory.services.initialization import ensure_initialize_database
+
+        ensure_initialize_database(config)
+
 
 # Register sub-command groups
 import_app = typer.Typer(help="Import data from various sources")

src/basic_memory/cli/commands/mcp.py

@@ -1,10 +1,7 @@
 """MCP server command."""
 
-from loguru import logger
-
 import basic_memory
 from basic_memory.cli.app import app
-from basic_memory.config import config, config_manager
 
 # Import mcp instance
 from basic_memory.mcp.server import mcp as mcp_server  # pragma: no cover
@@ -15,19 +12,24 @@
 
 @app.command()
 def mcp():  # pragma: no cover
-    """Run the MCP server for Claude Desktop integration."""
-    home_dir = config.home
-    project_name = config.project
+    """Run the MCP server"""
+    from basic_memory.config import config
+    import asyncio
+    from basic_memory.services.initialization import initialize_database
+
+    # First, run just the database migrations synchronously
+    asyncio.run(initialize_database(config))
+
+    # Load config to check if sync is enabled
+    from basic_memory.config import config_manager
 
-    # app config
     basic_memory_config = config_manager.load_config()
 
-    logger.info(f"Starting Basic Memory MCP server {basic_memory.__version__}")
-    logger.info(f"Project: {project_name}")
-    logger.info(f"Project directory: {home_dir}")
-    logger.info(f"Sync changes enabled: {basic_memory_config.sync_changes}")
-    logger.info(
-        f"Update permalinks on move enabled: {basic_memory_config.update_permalinks_on_move}"
-    )
+    if basic_memory_config.sync_changes:
+        # For now, we'll just log that sync will be handled by the MCP server
+        from loguru import logger
+
+        logger.info("File sync will be handled by the MCP server")
 
+    # Start the MCP server
     mcp_server.run()

src/basic_memory/cli/commands/sync.py

@@ -179,14 +179,14 @@ async def run_sync(verbose: bool = False, watch: bool = False, console_status: b
         )
 
         # full sync - no progress bars in watch mode
-        await sync_service.sync(config.home, show_progress=False)
+        await sync_service.sync(config.home)
 
         # watch changes
         await watch_service.run()  # pragma: no cover
     else:
-        # one time sync - use progress bars for better UX
+        # one time sync
         logger.info("Running one-time sync")
-        knowledge_changes = await sync_service.sync(config.home, show_progress=True)
+        knowledge_changes = await sync_service.sync(config.home)
 
         # Log results
         duration_ms = int((time.time() - start_time) * 1000)
@@ -237,11 +237,11 @@ def sync(
         if not isinstance(e, typer.Exit):
             logger.exception(
                 "Sync command failed",
-                project=config.project,
-                error=str(e),
-                error_type=type(e).__name__,
-                watch_mode=watch,
-                directory=str(config.home),
+                f"project={config.project},"
+                f"error={str(e)},"
+                f"error_type={type(e).__name__},"
+                f"watch_mode={watch},"
+                f"directory={str(config.home)}",
             )
             typer.echo(f"Error during sync: {e}", err=True)
             raise typer.Exit(1)

src/basic_memory/cli/main.py

@@ -1,9 +1,5 @@
 """Main CLI entry point for basic-memory."""  # pragma: no cover
 
-import asyncio
-
-import typer
-
 from basic_memory.cli.app import app  # pragma: no cover
 
 # Register commands
@@ -20,48 +16,11 @@
     tool,
 )
 from basic_memory.config import config
-from basic_memory.db import run_migrations as db_run_migrations
-
-
-# Version command
-@app.callback(invoke_without_command=True)
-def main(
-    ctx: typer.Context,
-    project: str = typer.Option(  # noqa
-        "main",
-        "--project",
-        "-p",
-        help="Specify which project to use",
-        envvar="BASIC_MEMORY_PROJECT",
-    ),
-    version: bool = typer.Option(
-        False,
-        "--version",
-        "-V",
-        help="Show version information and exit.",
-        is_eager=True,
-    ),
-):
-    """Basic Memory - Local-first personal knowledge management system."""
-    if version:  # pragma: no cover
-        from basic_memory import __version__
-        from basic_memory.config import config
-
-        typer.echo(f"Basic Memory v{__version__}")
-        typer.echo(f"Current project: {config.project}")
-        typer.echo(f"Project path: {config.home}")
-        raise typer.Exit()
-
-    # Handle project selection via environment variable
-    if project:
-        import os
-
-        os.environ["BASIC_MEMORY_PROJECT"] = project
-
+from basic_memory.services.initialization import ensure_initialization
 
 if __name__ == "__main__":  # pragma: no cover
-    # Run database migrations
-    asyncio.run(db_run_migrations(config))
+    # Run initialization if we are starting as a module
+    ensure_initialization(config)
 
     # start the app
     app()

src/basic_memory/config.py

@@ -35,7 +35,7 @@ class ProjectConfig(BaseSettings):
 
     # Watch service configuration
     sync_delay: int = Field(
-        default=500, description="Milliseconds to wait after changes before syncing", gt=0
+        default=1000, description="Milliseconds to wait after changes before syncing", gt=0
     )
 
     # update permalinks on move
@@ -274,7 +274,7 @@ def setup_basic_memory_logging():  # pragma: no cover
         console=False,
     )
 
-    logger.info(f"Starting Basic Memory {basic_memory.__version__} (Project: {config.project})")
+    logger.info(f"Basic Memory {basic_memory.__version__} (Project: {config.project})")
     _LOGGING_SETUP = True