fix: prevent CLI commands from hanging on exit (#471)

Signed-off-by: phernandez <paul@basicmachines.co>
Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com>

src/basic_memory/alembic/versions/f8a9b2c3d4e5_add_pg_trgm_for_fuzzy_link_resolution.py

@@ -10,6 +10,42 @@ from typing import Sequence, Union
 
 import sqlalchemy as sa
 from alembic import op
+from sqlalchemy import text
+
+
+def column_exists(connection, table: str, column: str) -> bool:
+    """Check if a column exists in a table (idempotent migration support)."""
+    if connection.dialect.name == "postgresql":
+        result = connection.execute(
+            text(
+                "SELECT 1 FROM information_schema.columns "
+                "WHERE table_name = :table AND column_name = :column"
+            ),
+            {"table": table, "column": column},
+        )
+        return result.fetchone() is not None
+    else:
+        # SQLite
+        result = connection.execute(text(f"PRAGMA table_info({table})"))
+        columns = [row[1] for row in result]
+        return column in columns
+
+
+def index_exists(connection, index_name: str) -> bool:
+    """Check if an index exists (idempotent migration support)."""
+    if connection.dialect.name == "postgresql":
+        result = connection.execute(
+            text("SELECT 1 FROM pg_indexes WHERE indexname = :index_name"),
+            {"index_name": index_name},
+        )
+        return result.fetchone() is not None
+    else:
+        # SQLite
+        result = connection.execute(
+            text("SELECT 1 FROM sqlite_master WHERE type='index' AND name = :index_name"),
+            {"index_name": index_name},
+        )
+        return result.fetchone() is not None
 
 
 # revision identifiers, used by Alembic.
@@ -36,101 +72,105 @@ def upgrade() -> None:
     # Add project_id to relation table
     # -------------------------------------------------------------------------
 
-    # Step 1: Add project_id column as nullable first
-    op.add_column("relation", sa.Column("project_id", sa.Integer(), nullable=True))
+    # Step 1: Add project_id column as nullable first (idempotent)
+    if not column_exists(connection, "relation", "project_id"):
+        op.add_column("relation", sa.Column("project_id", sa.Integer(), nullable=True))
 
-    # Step 2: Backfill project_id from entity.project_id via from_id
-    if dialect == "postgresql":
-        op.execute("""
-            UPDATE relation
-            SET project_id = entity.project_id
-            FROM entity
-            WHERE relation.from_id = entity.id
-        """)
-    else:
-        # SQLite syntax
-        op.execute("""
-            UPDATE relation
-            SET project_id = (
-                SELECT entity.project_id
+        # Step 2: Backfill project_id from entity.project_id via from_id
+        if dialect == "postgresql":
+            op.execute("""
+                UPDATE relation
+                SET project_id = entity.project_id
                 FROM entity
-                WHERE entity.id = relation.from_id
-            )
-        """)
+                WHERE relation.from_id = entity.id
+            """)
+        else:
+            # SQLite syntax
+            op.execute("""
+                UPDATE relation
+                SET project_id = (
+                    SELECT entity.project_id
+                    FROM entity
+                    WHERE entity.id = relation.from_id
+                )
+            """)
 
-    # Step 3: Make project_id NOT NULL and add foreign key
-    if dialect == "postgresql":
-        op.alter_column("relation", "project_id", nullable=False)
-        op.create_foreign_key(
-            "fk_relation_project_id",
-            "relation",
-            "project",
-            ["project_id"],
-            ["id"],
-        )
-    else:
-        # SQLite requires batch operations for ALTER COLUMN
-        with op.batch_alter_table("relation") as batch_op:
-            batch_op.alter_column("project_id", nullable=False)
-            batch_op.create_foreign_key(
+        # Step 3: Make project_id NOT NULL and add foreign key
+        if dialect == "postgresql":
+            op.alter_column("relation", "project_id", nullable=False)
+            op.create_foreign_key(
                 "fk_relation_project_id",
+                "relation",
                 "project",
                 ["project_id"],
                 ["id"],
             )
+        else:
+            # SQLite requires batch operations for ALTER COLUMN
+            with op.batch_alter_table("relation") as batch_op:
+                batch_op.alter_column("project_id", nullable=False)
+                batch_op.create_foreign_key(
+                    "fk_relation_project_id",
+                    "project",
+                    ["project_id"],
+                    ["id"],
+                )
 
-    # Step 4: Create index on relation.project_id
-    op.create_index("ix_relation_project_id", "relation", ["project_id"])
+    # Step 4: Create index on relation.project_id (idempotent)
+    if not index_exists(connection, "ix_relation_project_id"):
+        op.create_index("ix_relation_project_id", "relation", ["project_id"])
 
     # -------------------------------------------------------------------------
     # Add project_id to observation table
     # -------------------------------------------------------------------------
 
-    # Step 1: Add project_id column as nullable first
-    op.add_column("observation", sa.Column("project_id", sa.Integer(), nullable=True))
+    # Step 1: Add project_id column as nullable first (idempotent)
+    if not column_exists(connection, "observation", "project_id"):
+        op.add_column("observation", sa.Column("project_id", sa.Integer(), nullable=True))
 
-    # Step 2: Backfill project_id from entity.project_id via entity_id
-    if dialect == "postgresql":
-        op.execute("""
-            UPDATE observation
-            SET project_id = entity.project_id
-            FROM entity
-            WHERE observation.entity_id = entity.id
-        """)
-    else:
-        # SQLite syntax
-        op.execute("""
-            UPDATE observation
-            SET project_id = (
-                SELECT entity.project_id
+        # Step 2: Backfill project_id from entity.project_id via entity_id
+        if dialect == "postgresql":
+            op.execute("""
+                UPDATE observation
+                SET project_id = entity.project_id
                 FROM entity
-                WHERE entity.id = observation.entity_id
-            )
-        """)
+                WHERE observation.entity_id = entity.id
+            """)
+        else:
+            # SQLite syntax
+            op.execute("""
+                UPDATE observation
+                SET project_id = (
+                    SELECT entity.project_id
+                    FROM entity
+                    WHERE entity.id = observation.entity_id
+                )
+            """)
 
-    # Step 3: Make project_id NOT NULL and add foreign key
-    if dialect == "postgresql":
-        op.alter_column("observation", "project_id", nullable=False)
-        op.create_foreign_key(
-            "fk_observation_project_id",
-            "observation",
-            "project",
-            ["project_id"],
-            ["id"],
-        )
-    else:
-        # SQLite requires batch operations for ALTER COLUMN
-        with op.batch_alter_table("observation") as batch_op:
-            batch_op.alter_column("project_id", nullable=False)
-            batch_op.create_foreign_key(
+        # Step 3: Make project_id NOT NULL and add foreign key
+        if dialect == "postgresql":
+            op.alter_column("observation", "project_id", nullable=False)
+            op.create_foreign_key(
                 "fk_observation_project_id",
+                "observation",
                 "project",
                 ["project_id"],
                 ["id"],
             )
+        else:
+            # SQLite requires batch operations for ALTER COLUMN
+            with op.batch_alter_table("observation") as batch_op:
+                batch_op.alter_column("project_id", nullable=False)
+                batch_op.create_foreign_key(
+                    "fk_observation_project_id",
+                    "project",
+                    ["project_id"],
+                    ["id"],
+                )
 
-    # Step 4: Create index on observation.project_id
-    op.create_index("ix_observation_project_id", "observation", ["project_id"])
+    # Step 4: Create index on observation.project_id (idempotent)
+    if not index_exists(connection, "ix_observation_project_id"):
+        op.create_index("ix_observation_project_id", "observation", ["project_id"])
 
     # Postgres-specific: pg_trgm and GIN indexes
     if dialect == "postgresql":

src/basic_memory/api/app.py

@@ -1,6 +1,7 @@
 """FastAPI application for basic-memory knowledge graph API."""
 
 import asyncio
+import os
 from contextlib import asynccontextmanager
 
 from fastapi import FastAPI, HTTPException
@@ -53,12 +54,25 @@ async def lifespan(app: FastAPI):  # pragma: no cover
     app.state.session_maker = session_maker
     logger.info("Database connections cached in app state")
 
-    logger.info(f"Sync changes enabled: {app_config.sync_changes}")
-    if app_config.sync_changes:
+    # Start file sync if enabled
+    is_test_env = (
+        app_config.env == "test"
+        or os.getenv("BASIC_MEMORY_ENV", "").lower() == "test"
+        or os.getenv("PYTEST_CURRENT_TEST") is not None
+    )
+    if app_config.sync_changes and not is_test_env:
+        logger.info(f"Sync changes enabled: {app_config.sync_changes}")
+
         # start file sync task in background
-        app.state.sync_task = asyncio.create_task(initialize_file_sync(app_config))
+        async def _file_sync_runner() -> None:
+            await initialize_file_sync(app_config)
+
+        app.state.sync_task = asyncio.create_task(_file_sync_runner())
     else:
-        logger.info("Sync changes disabled. Skipping file sync service.")
+        if is_test_env:
+            logger.info("Test environment detected. Skipping file sync service.")
+        else:
+            logger.info("Sync changes disabled. Skipping file sync service.")
         app.state.sync_task = None
 
     # proceed with startup

src/basic_memory/cli/app.py

@@ -34,8 +34,15 @@ def app_callback(
     # Initialize logging for CLI (file only, no stdout)
     init_cli_logging()
 
-    # Run initialization for every command unless --version was specified
-    if not version and ctx.invoked_subcommand is not None:
+    # 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"}
+    if (
+        not version
+        and ctx.invoked_subcommand is not None
+        and ctx.invoked_subcommand not in api_commands
+    ):
         from basic_memory.services.initialization import ensure_initialization
 
         app_config = ConfigManager().config

src/basic_memory/cli/commands/command_utils.py

@@ -1,12 +1,14 @@
 """utility functions for commands"""
 
-from typing import Optional
+import asyncio
+from typing import Optional, TypeVar, Coroutine, Any
 
 from mcp.server.fastmcp.exceptions import ToolError
 import typer
 
 from rich.console import Console
 
+from basic_memory import db
 from basic_memory.mcp.async_client import get_client
 
 from basic_memory.mcp.tools.utils import call_post, call_get
@@ -15,6 +17,30 @@ from basic_memory.schemas import ProjectInfoResponse
 
 console = Console()
 
+T = TypeVar("T")
+
+
+def run_with_cleanup(coro: Coroutine[Any, Any, T]) -> T:
+    """Run an async coroutine with proper database cleanup.
+
+    This helper ensures database connections are cleaned up before the event
+    loop closes, preventing process hangs in CLI commands.
+
+    Args:
+        coro: The coroutine to run
+
+    Returns:
+        The result of the coroutine
+    """
+
+    async def _with_cleanup() -> T:
+        try:
+            return await coro
+        finally:
+            await db.shutdown_db()
+
+    return asyncio.run(_with_cleanup())
+
 
 async def run_sync(project: Optional[str] = None, force_full: bool = False):
     """Run sync operation via API endpoint.

src/basic_memory/cli/commands/mcp.py

@@ -1,6 +1,5 @@
 """MCP server command with streamable HTTP transport."""
 
-import asyncio
 import os
 import typer
 from typing import Optional
@@ -8,7 +7,7 @@ from typing import Optional
 from basic_memory.cli.app import app
 from basic_memory.config import ConfigManager, init_mcp_logging
 
-# Import mcp instance
+# Import mcp instance (has lifespan that handles initialization and file sync)
 from basic_memory.mcp.server import mcp as mcp_server  # pragma: no cover
 
 # Import mcp tools to register them
@@ -17,8 +16,6 @@ import basic_memory.mcp.tools  # noqa: F401  # pragma: no cover
 # Import prompts to register them
 import basic_memory.mcp.prompts  # noqa: F401  # pragma: no cover
 from loguru import logger
-import threading
-from basic_memory.services.initialization import initialize_file_sync
 
 config = ConfigManager().config
 
@@ -43,6 +40,8 @@ if not config.cloud_mode_enabled:
         - stdio: Standard I/O (good for local usage)
         - streamable-http: Recommended for web deployments (default)
         - sse: Server-Sent Events (for compatibility with existing clients)
+
+        Initialization, file sync, and cleanup are handled by the MCP server's lifespan.
         """
         # Initialize logging for MCP (file only, stdout breaks protocol)
         init_mcp_logging()
@@ -59,27 +58,8 @@ if not config.cloud_mode_enabled:
             os.environ["BASIC_MEMORY_MCP_PROJECT"] = project_name
             logger.info(f"MCP server constrained to project: {project_name}")
 
-        app_config = ConfigManager().config
-
-        def run_file_sync():
-            """Run file sync in a separate thread with its own event loop."""
-            loop = asyncio.new_event_loop()
-            asyncio.set_event_loop(loop)
-            try:
-                loop.run_until_complete(initialize_file_sync(app_config))
-            except Exception as e:
-                logger.error(f"File sync error: {e}", err=True)
-            finally:
-                loop.close()
-
-        logger.info(f"Sync changes enabled: {app_config.sync_changes}")
-        if app_config.sync_changes:
-            # Start the sync thread
-            sync_thread = threading.Thread(target=run_file_sync, daemon=True)
-            sync_thread.start()
-            logger.info("Started file sync in background")
-
-        # Now run the MCP server (blocks)
+        # Run the MCP server (blocks)
+        # Lifespan handles: initialization, migrations, file sync, cleanup
         logger.info(f"Starting MCP server with {transport.upper()} transport")
 
         if transport == "stdio":

src/basic_memory/cli/commands/status.py

@@ -1,6 +1,5 @@
 """Status command for basic-memory CLI."""
 
-import asyncio
 from typing import Set, Dict
 from typing import Annotated, Optional
 
@@ -165,8 +164,10 @@ def status(
     verbose: bool = typer.Option(False, "--verbose", "-v", help="Show detailed file information"),
 ):
     """Show sync status between files and database."""
+    from basic_memory.cli.commands.command_utils import run_with_cleanup
+
     try:
-        asyncio.run(run_status(project, verbose))  # pragma: no cover
+        run_with_cleanup(run_status(project, verbose))  # pragma: no cover
     except Exception as e:
         logger.error(f"Error checking status: {e}")
         typer.echo(f"Error checking status: {e}", err=True)

src/basic_memory/db.py

@@ -1,5 +1,6 @@
 import asyncio
 import os
+import sys
 from contextlib import asynccontextmanager
 from enum import Enum, auto
 from pathlib import Path
@@ -23,6 +24,21 @@ from sqlalchemy.pool import NullPool
 from basic_memory.repository.postgres_search_repository import PostgresSearchRepository
 from basic_memory.repository.sqlite_search_repository import SQLiteSearchRepository
 
+# -----------------------------------------------------------------------------
+# Windows event loop policy
+# -----------------------------------------------------------------------------
+# On Windows, the default ProactorEventLoop has known rough edges with aiosqlite
+# during shutdown/teardown (threads posting results to a loop that's closing),
+# which can manifest as:
+# - "RuntimeError: Event loop is closed"
+# - "IndexError: pop from an empty deque"
+#
+# The SelectorEventLoop doesn't support subprocess operations, so code that uses
+# asyncio.create_subprocess_shell() (like sync_service._quick_count_files) must
+# detect Windows and use fallback implementations.
+if sys.platform == "win32":  # pragma: no cover
+    asyncio.set_event_loop_policy(asyncio.WindowsSelectorEventLoopPolicy())
+
 # Module level state
 _engine: Optional[AsyncEngine] = None
 _session_maker: Optional[async_sessionmaker[AsyncSession]] = None

src/basic_memory/mcp/async_client.py

@@ -95,6 +95,7 @@ async def get_client() -> AsyncIterator[AsyncClient]:
                 yield client
         else:
             # Local mode: ASGI transport for in-process calls
+            # Note: ASGI transport does NOT trigger FastAPI lifespan, so no special handling needed
             logger.info("Creating ASGI client for local Basic Memory API")
             async with AsyncClient(
                 transport=ASGITransport(app=fastapi_app), base_url="http://test", timeout=timeout

src/basic_memory/mcp/server.py

@@ -2,8 +2,80 @@
 Basic Memory FastMCP server.
 """
 
+import asyncio
+import os
+from contextlib import asynccontextmanager
+
 from fastmcp import FastMCP
+from loguru import logger
+
+from basic_memory import db
+from basic_memory.config import ConfigManager
+from basic_memory.services.initialization import initialize_app, initialize_file_sync
+
+
+@asynccontextmanager
+async def lifespan(app: FastMCP):
+    """Lifecycle manager for the MCP server.
+
+    Handles:
+    - Database initialization and migrations
+    - File sync in background (if enabled and not in cloud mode)
+    - Proper cleanup on shutdown
+    """
+    app_config = ConfigManager().config
+    logger.info("Starting Basic Memory MCP server")
+
+    # Track if we created the engine (vs test fixtures providing it)
+    # This prevents disposing an engine provided by test fixtures when
+    # multiple Client connections are made in the same test
+    engine_was_none = db._engine is None
+
+    # Initialize app (runs migrations, reconciles projects)
+    await initialize_app(app_config)
+
+    # Start file sync as background task (if enabled and not in cloud mode)
+    sync_task = None
+    is_test_env = (
+        app_config.env == "test"
+        or os.getenv("BASIC_MEMORY_ENV", "").lower() == "test"
+        or os.getenv("PYTEST_CURRENT_TEST") is not None
+    )
+    if is_test_env:
+        logger.info("Test environment detected - skipping local file sync")
+    elif app_config.sync_changes and not app_config.cloud_mode_enabled:
+        logger.info("Starting file sync in background")
+
+        async def _file_sync_runner() -> None:
+            await initialize_file_sync(app_config)
+
+        sync_task = asyncio.create_task(_file_sync_runner())
+    elif app_config.cloud_mode_enabled:
+        logger.info("Cloud mode enabled - skipping local file sync")
+    else:
+        logger.info("Sync changes disabled - skipping file sync")
+
+    try:
+        yield
+    finally:
+        # Shutdown
+        logger.info("Shutting down Basic Memory MCP server")
+        if sync_task:
+            sync_task.cancel()
+            try:
+                await sync_task
+            except asyncio.CancelledError:
+                logger.info("File sync task cancelled")
+
+        # Only shutdown DB if we created it (not if test fixture provided it)
+        if engine_was_none:
+            await db.shutdown_db()
+            logger.info("Database connections closed")
+        else:
+            logger.debug("Skipping DB shutdown - engine provided externally")
+
 
 mcp = FastMCP(
     name="Basic Memory",
+    lifespan=lifespan,
 )

src/basic_memory/services/initialization.py

@@ -6,6 +6,7 @@ to ensure consistent application startup across all entry points.
 
 import asyncio
 import os
+import sys
 from pathlib import Path
 
 
@@ -29,15 +30,12 @@ async def initialize_database(app_config: BasicMemoryConfig) -> None:
         Database migrations are now handled automatically when the database
         connection is first established via get_or_create_db().
     """
-    # Trigger database initialization and migrations by getting the database connection
     try:
         await db.get_or_create_db(app_config.database_path)
         logger.info("Database initialization completed")
     except Exception as e:
-        logger.error(f"Error initializing database: {e}")
-        # Allow application to continue - it might still work
-        # depending on what the error was, and will fail with a
-        # more specific error if the database is actually unusable
+        logger.error(f"Error during database initialization: {e}")
+        raise
 
 
 async def reconcile_projects_with_config(app_config: BasicMemoryConfig):
@@ -51,31 +49,29 @@ async def reconcile_projects_with_config(app_config: BasicMemoryConfig):
     """
     logger.info("Reconciling projects from config with database...")
 
-    # Get database session - migrations handled centrally
+    # Get database session (engine already created by initialize_database)
     _, session_maker = await db.get_or_create_db(
         db_path=app_config.database_path,
         db_type=db.DatabaseType.FILESYSTEM,
-        ensure_migrations=False,
     )
     project_repository = ProjectRepository(session_maker)
 
     # Import ProjectService here to avoid circular imports
     from basic_memory.services.project_service import ProjectService
 
+    # Create project service and synchronize projects
+    project_service = ProjectService(repository=project_repository)
     try:
-        # Create project service and synchronize projects
-        project_service = ProjectService(repository=project_repository)
         await project_service.synchronize_projects()
         logger.info("Projects successfully reconciled between config and database")
     except Exception as e:
-        # Log the error but continue with initialization
         logger.error(f"Error during project synchronization: {e}")
         logger.info("Continuing with initialization despite synchronization error")
 
 
 async def initialize_file_sync(
     app_config: BasicMemoryConfig,
-):
+) -> None:
     """Initialize file synchronization services. This function starts the watch service and does not return
 
     Args:
@@ -84,15 +80,26 @@ async def initialize_file_sync(
     Returns:
         The watch service task that's monitoring file changes
     """
+    # Never start file watching during tests. Even "background" watchers add tasks/threads
+    # and can interact badly with strict asyncio teardown (especially on Windows/aiosqlite).
+    #
+    # Note: Some tests patch ConfigManager.config with a minimal BasicMemoryConfig that
+    # may not set env="test". So also detect pytest via env vars.
+    if (
+        app_config.env == "test"
+        or os.getenv("BASIC_MEMORY_ENV", "").lower() == "test"
+        or os.getenv("PYTEST_CURRENT_TEST") is not None
+    ):
+        logger.info("Test environment detected - skipping file sync initialization")
+        return None
 
     # delay import
     from basic_memory.sync import WatchService
 
-    # Load app configuration - migrations handled centrally
+    # Get database session (migrations already run if needed)
     _, session_maker = await db.get_or_create_db(
         db_path=app_config.database_path,
         db_type=db.DatabaseType.FILESYSTEM,
-        ensure_migrations=False,
     )
     project_repository = ProjectRepository(session_maker)
 
@@ -139,12 +146,10 @@ async def initialize_file_sync(
 
     # Then start the watch service in the background
     logger.info("Starting watch service for all projects")
+
     # run the watch service
-    try:
-        await watch_service.run()
-        logger.info("Watch service started")
-    except Exception as e:  # pragma: no cover
-        logger.error(f"Error starting watch service: {e}")
+    await watch_service.run()
+    logger.info("Watch service started")
 
     return None
 
@@ -189,11 +194,24 @@ def ensure_initialization(app_config: BasicMemoryConfig) -> None:
         logger.debug("Skipping initialization in cloud mode - projects managed by cloud")
         return
 
-    try:
-        result = asyncio.run(initialize_app(app_config))
-        logger.info(f"Initialization completed successfully: result={result}")
-    except Exception as e:  # pragma: no cover
-        logger.exception(f"Error during initialization: {e}")
-        # Continue execution even if initialization fails
-        # The command might still work, or will fail with a
-        # more specific error message
+    async def _init_and_cleanup():
+        """Initialize app and clean up database connections.
+
+        Database connections created during initialization must be cleaned up
+        before the event loop closes, otherwise the process will hang indefinitely.
+        """
+        try:
+            await initialize_app(app_config)
+        finally:
+            # Always cleanup database connections to prevent process hang
+            await db.shutdown_db()
+
+    # On Windows, use SelectorEventLoop to avoid ProactorEventLoop cleanup issues
+    # The ProactorEventLoop can raise "IndexError: pop from an empty deque" during
+    # event loop cleanup when there are pending handles. SelectorEventLoop is more
+    # stable for our use case (no subprocess pipes or named pipes needed).
+    if sys.platform == "win32":
+        asyncio.set_event_loop_policy(asyncio.WindowsSelectorEventLoopPolicy())
+
+    asyncio.run(_init_and_cleanup())
+    logger.info("Initialization completed successfully")

src/basic_memory/sync/sync_service.py

@@ -2,6 +2,7 @@
 
 import asyncio
 import os
+import sys
 import time
 from collections import OrderedDict
 from dataclasses import dataclass, field
@@ -1027,12 +1028,22 @@ class SyncService:
         Uses subprocess to leverage OS-level file counting which is much faster
         than Python iteration, especially on network filesystems like TigrisFS.
 
+        On Windows, subprocess is not supported with SelectorEventLoop (which we use
+        to avoid aiosqlite cleanup issues), so we fall back to Python-based counting.
+
         Args:
             directory: Directory to count files in
 
         Returns:
             Number of files in directory (recursive)
         """
+        # Windows with SelectorEventLoop doesn't support subprocess
+        if sys.platform == "win32":
+            count = 0
+            async for _ in self.scan_directory(directory):
+                count += 1
+            return count
+
         process = await asyncio.create_subprocess_shell(
             f'find "{directory}" -type f | wc -l',
             stdout=asyncio.subprocess.PIPE,
@@ -1063,6 +1074,9 @@ class SyncService:
         This is dramatically faster than scanning all files and comparing mtimes,
         especially on network filesystems like TigrisFS where stat operations are expensive.
 
+        On Windows, subprocess is not supported with SelectorEventLoop (which we use
+        to avoid aiosqlite cleanup issues), so we implement mtime filtering in Python.
+
         Args:
             directory: Directory to scan
             since_timestamp: Unix timestamp to find files newer than
@@ -1070,6 +1084,16 @@ class SyncService:
         Returns:
             List of relative file paths modified since the timestamp (respects .bmignore)
         """
+        # Windows with SelectorEventLoop doesn't support subprocess
+        # Implement mtime filtering in Python to preserve watermark optimization
+        if sys.platform == "win32":
+            file_paths = []
+            async for file_path_str, stat_info in self.scan_directory(directory):
+                if stat_info.st_mtime > since_timestamp:
+                    rel_path = Path(file_path_str).relative_to(directory).as_posix()
+                    file_paths.append(rel_path)
+            return file_paths
+
         # Convert timestamp to find-compatible format
         since_date = datetime.fromtimestamp(since_timestamp).strftime("%Y-%m-%d %H:%M:%S")
 

src/basic_memory/utils.py

@@ -232,6 +232,8 @@ def setup_logging(
     if log_to_file:
         log_path = Path.home() / ".basic-memory" / "basic-memory.log"
         log_path.parent.mkdir(parents=True, exist_ok=True)
+        # Keep logging synchronous (enqueue=False) to avoid background logging threads.
+        # Background threads are a common source of "hang on exit" issues in CLI/test runs.
         logger.add(
             str(log_path),
             level=log_level,
@@ -239,7 +241,7 @@ def setup_logging(
             retention="10 days",
             backtrace=True,
             diagnose=True,
-            enqueue=True,  # Thread-safe async logging
+            enqueue=False,
             colorize=False,
         )