fix: improve reset command reliability and UX

- Skip database initialization for reset command (like mcp/status/etc)
- Delete WAL files (-shm, -wal) along with main database file
- Add user-friendly error messages when database is locked
- Show reassuring message that note files won't be deleted

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <[email protected]>
Signed-off-by: phernandez <[email protected]>

Author: phernandez

src/basic_memory/cli/app.py

@@ -63,11 +63,12 @@ def app_callback(
     # Run initialization for commands that don't use the API
     # Skip for 'mcp' command - it has its own lifespan that handles initialization
     # Skip for API-using commands (status, sync, etc.) - they handle initialization via deps.py
-    api_commands = {"mcp", "status", "sync", "project", "tool"}
+    # Skip for 'reset' command - it manages its own database lifecycle
+    skip_init_commands = {"mcp", "status", "sync", "project", "tool", "reset"}
     if (
         not version
         and ctx.invoked_subcommand is not None
-        and ctx.invoked_subcommand not in api_commands
+        and ctx.invoked_subcommand not in skip_init_commands
     ):
         from basic_memory.services.initialization import ensure_initialization
 

src/basic_memory/cli/commands/db.py

@@ -4,36 +4,64 @@
 
 import typer
 from loguru import logger
+from rich.console import Console
+from sqlalchemy.exc import OperationalError
 
 from basic_memory import db
 from basic_memory.cli.app import app
 from basic_memory.config import ConfigManager, BasicMemoryConfig, save_basic_memory_config
 
+console = Console()
+
 
 @app.command()
 def reset(
     reindex: bool = typer.Option(False, "--reindex", help="Rebuild db index from filesystem"),
 ):  # pragma: no cover
     """Reset database (drop all tables and recreate)."""
-    if typer.confirm("This will delete all data in your db. Are you sure?"):
+    console.print(
+        "[yellow]Note:[/yellow] This only deletes the index database. "
+        "Your markdown note files will not be affected."
+    )
+    if typer.confirm("Reset the database index? (You can rebuild it with 'bm sync')"):
         logger.info("Resetting database...")
         config_manager = ConfigManager()
         app_config = config_manager.config
         # Get database path
         db_path = app_config.app_database_path
 
-        # Delete the database file if it exists
-        if db_path.exists():
-            db_path.unlink()
-            logger.info(f"Database file deleted: {db_path}")
+        # Delete the database file and WAL files if they exist
+        for suffix in ["", "-shm", "-wal"]:
+            path = db_path.parent / f"{db_path.name}{suffix}"
+            if path.exists():
+                try:
+                    path.unlink()
+                    logger.info(f"Deleted: {path}")
+                except OSError as e:
+                    console.print(
+                        f"[red]Error:[/red] Cannot delete {path.name}: {e}\n"
+                        "The database may be in use by another process (e.g., MCP server).\n"
+                        "Please close Claude Desktop or any other Basic Memory clients and try again."
+                    )
+                    raise typer.Exit(1)
 
         # Reset project configuration
         config = BasicMemoryConfig()
         save_basic_memory_config(config_manager.config_file, config)
         logger.info("Project configuration reset to default")
 
         # Create a new empty database
-        asyncio.run(db.run_migrations(app_config))
+        try:
+            asyncio.run(db.run_migrations(app_config))
+        except OperationalError as e:
+            if "disk I/O error" in str(e) or "database is locked" in str(e):
+                console.print(
+                    "[red]Error:[/red] Cannot access database. "
+                    "It may be in use by another process (e.g., MCP server).\n"
+                    "Please close Claude Desktop or any other Basic Memory clients and try again."
+                )
+                raise typer.Exit(1)
+            raise
         logger.info("Database reset complete")
 
         if reindex: