diff --git a/src/cocoindex_code/cli.py b/src/cocoindex_code/cli.py
index 3cb973e..dde76a0 100644
--- a/src/cocoindex_code/cli.py
+++ b/src/cocoindex_code/cli.py
@@ -287,16 +287,29 @@ def daemon_restart() -> None:
 @daemon_app.command("stop")
 def daemon_stop() -> None:
     """Stop the daemon."""
-    from .client import DaemonClient
+    from .client import stop_daemon
+    from .daemon import daemon_pid_path
 
-    try:
-        client = DaemonClient.connect()
-        client.handshake()
-        client.stop()
-        client.close()
-        _typer.echo("Daemon stopped.")
-    except (ConnectionRefusedError, OSError):
+    pid_path = daemon_pid_path()
+    if not pid_path.exists():
         _typer.echo("Daemon is not running.")
+        return
+
+    stop_daemon()
+
+    # Wait for process to exit
+    import time
+
+    deadline = time.monotonic() + 5.0
+    while time.monotonic() < deadline:
+        if not pid_path.exists():
+            break
+        time.sleep(0.1)
+
+    if pid_path.exists():
+        _typer.echo("Warning: daemon may not have stopped cleanly.", err=True)
+    else:
+        _typer.echo("Daemon stopped.")
 
 
 @app.command("run-daemon", hidden=True)
diff --git a/src/cocoindex_code/client.py b/src/cocoindex_code/client.py
index f62b05c..e0fdb36 100644
--- a/src/cocoindex_code/client.py
+++ b/src/cocoindex_code/client.py
@@ -162,26 +162,43 @@ def _find_ccc_executable() -> str | None:
 
 
 def stop_daemon() -> None:
-    """Stop the daemon gracefully."""
+    """Stop the daemon gracefully.
+
+    Sends a StopRequest, waits for the process to exit, falls back to SIGTERM.
+    """
+    # Step 1: try sending StopRequest
     try:
         client = DaemonClient.connect()
         client.handshake()
         client.stop()
         client.close()
-    except (ConnectionRefusedError, OSError):
+    except (ConnectionRefusedError, OSError, RuntimeError):
         pass
 
-    # If daemon doesn't respond, try SIGTERM via PID
+    # Step 2: wait for process to exit (up to 5s)
     pid_path = daemon_pid_path()
+    deadline = time.monotonic() + 5.0
+    while time.monotonic() < deadline and pid_path.exists():
+        time.sleep(0.1)
+
+    if not pid_path.exists():
+        return  # Clean exit
+
+    # Step 3: if still running, try SIGTERM
     if pid_path.exists():
         try:
             pid = int(pid_path.read_text().strip())
-            if pid != os.getpid():  # Never kill ourselves (happens when daemon runs in a thread)
+            if pid != os.getpid():
                 os.kill(pid, signal.SIGTERM)
         except (ValueError, ProcessLookupError, PermissionError):
             pass
 
-    # Clean up stale files (named pipes on Windows clean up automatically)
+        # Wait a bit more
+        deadline = time.monotonic() + 2.0
+        while time.monotonic() < deadline and pid_path.exists():
+            time.sleep(0.1)
+
+    # Step 4: clean up stale files
     if sys.platform != "win32":
         sock = daemon_socket_path()
         try:
diff --git a/src/cocoindex_code/daemon.py b/src/cocoindex_code/daemon.py
index 6660452..1fb5f7a 100644
--- a/src/cocoindex_code/daemon.py
+++ b/src/cocoindex_code/daemon.py
@@ -210,10 +210,18 @@ async def handle_connection(
     loop = asyncio.get_event_loop()
     handshake_done = False
 
+    def _recv() -> bytes:
+        """Blocking recv that also checks for shutdown."""
+        # Use poll with a timeout so we can check shutdown_event periodically
+        while not shutdown_event.is_set():
+            if conn.poll(0.5):
+                return conn.recv_bytes()
+        raise EOFError("shutdown")
+
     try:
         while not shutdown_event.is_set():
             try:
-                data: bytes = await loop.run_in_executor(None, conn.recv_bytes)
+                data: bytes = await loop.run_in_executor(None, _recv)
             except (EOFError, OSError):
                 break
 
diff --git a/src/cocoindex_code/server.py b/src/cocoindex_code/server.py
index 5eec11d..b1343a6 100644
--- a/src/cocoindex_code/server.py
+++ b/src/cocoindex_code/server.py
@@ -188,7 +188,7 @@ def main() -> None:
         LanguageOverride,
         default_project_settings,
         default_user_settings,
-        find_parent_with_marker,
+        find_legacy_project_root,
         find_project_root,
         project_settings_path,
         save_project_settings,
@@ -216,8 +216,8 @@ def main() -> None:
             project_root = Path(env_root).resolve()
         else:
             # Use marker-based discovery
-            marker_root = find_parent_with_marker(cwd)
-            project_root = marker_root if marker_root is not None else cwd
+            legacy_root = find_legacy_project_root(cwd)
+            project_root = legacy_root if legacy_root is not None else cwd
 
     # --- Auto-create project settings if needed ---
     proj_settings_file = project_settings_path(project_root)
diff --git a/src/cocoindex_code/settings.py b/src/cocoindex_code/settings.py
index 97f356a..fb5b8be 100644
--- a/src/cocoindex_code/settings.py
+++ b/src/cocoindex_code/settings.py
@@ -151,6 +151,22 @@ def find_project_root(start: Path) -> Path | None:
         current = parent
 
 
+def find_legacy_project_root(start: Path) -> Path | None:
+    """Walk up from *start* looking for a ``.cocoindex_code/`` dir that contains ``cocoindex.db``.
+
+    Used by the backward-compat ``cocoindex-code`` entrypoint to re-anchor to a
+    previously-indexed project tree.  Returns the first matching directory, or ``None``.
+    """
+    current = start.resolve()
+    while True:
+        if (current / _SETTINGS_DIR_NAME / "cocoindex.db").exists():
+            return current
+        parent = current.parent
+        if parent == current:
+            return None
+        current = parent
+
+
 def find_parent_with_marker(start: Path) -> Path | None:
     """Walk up from *start* looking for ``.cocoindex_code/`` or ``.git/``.
 
diff --git a/tests/test_backward_compat.py b/tests/test_backward_compat.py
index 96b4d67..09bb577 100644
--- a/tests/test_backward_compat.py
+++ b/tests/test_backward_compat.py
@@ -13,6 +13,7 @@
     UserSettings,
     default_project_settings,
     default_user_settings,
+    find_legacy_project_root,
     load_project_settings,
     load_user_settings,
     save_project_settings,
@@ -104,6 +105,27 @@ def test_legacy_extra_extensions_conversion(tmp_path: Path) -> None:
     assert "**/*.toml" in loaded.include_patterns
 
 
+def test_legacy_root_discovery_requires_cocoindex_db(tmp_path: Path) -> None:
+    """A .cocoindex_code dir without cocoindex.db should not be matched."""
+    (tmp_path / ".cocoindex_code").mkdir()
+    assert find_legacy_project_root(tmp_path) is None
+
+
+def test_legacy_root_discovery_with_cocoindex_db(tmp_path: Path) -> None:
+    """A .cocoindex_code dir with cocoindex.db should be matched, including from a subdirectory."""
+    idx_dir = tmp_path / ".cocoindex_code"
+    idx_dir.mkdir()
+    (idx_dir / "cocoindex.db").touch()
+
+    # Exact directory
+    assert find_legacy_project_root(tmp_path) == tmp_path
+
+    # From a subdirectory — should walk up and find the root
+    sub = tmp_path / "src" / "pkg"
+    sub.mkdir(parents=True)
+    assert find_legacy_project_root(sub) == tmp_path
+
+
 def test_legacy_excluded_patterns_conversion(tmp_path: Path) -> None:
     """COCOINDEX_CODE_EXCLUDED_PATTERNS should be appended to default exclude_patterns."""