Fix switch_modes tool silently failing to change modes

set_modes() applied requested modes directly to self._active_modes,
then called _update_active_modes_and_tools() which recreates
_active_modes from scratch (global config -> project config -> CLI
overrides), discarding the change.

Fix: store the requested modes into self._mode_overrides so they
survive the rebuild and take highest priority, matching the behavior
of CLI --mode flags.

Also adds test coverage for set_modes() which was previously untested.

Bug was introduced in commit 40a3075 on Jan 26, 2026.

src/serena/agent.py

@@ -522,7 +522,7 @@ class SerenaAgent:
 
         :param mode_names: List of mode names or paths to use
         """
-        self._active_modes.apply(ModeSelectionDefinition(default_modes=mode_names))
+        self._mode_overrides = ModeSelectionDefinition(default_modes=mode_names)
         self._update_active_modes_and_tools()
 
         log.info(f"Set modes to {[mode.name for mode in self.get_active_modes()]}")

test/serena/test_set_modes.py

@@ -0,0 +1,75 @@
+"""Tests for SerenaAgent.set_modes() to verify that mode switching works correctly."""
+
+import logging
+
+from serena.agent import SerenaAgent
+from serena.config.serena_config import ModeSelectionDefinition, SerenaConfig
+
+
+class TestSetModes:
+    """Test that set_modes correctly changes active modes."""
+
+    def _create_agent(self, modes: ModeSelectionDefinition | None = None) -> SerenaAgent:
+        config = SerenaConfig(gui_log_window=False, web_dashboard=False, log_level=logging.ERROR)
+        return SerenaAgent(serena_config=config, modes=modes)
+
+    def test_set_modes_changes_active_modes(self) -> None:
+        """Test that calling set_modes actually changes the active modes."""
+        agent = self._create_agent(modes=ModeSelectionDefinition(default_modes=["editing", "interactive"]))
+
+        initial_mode_names = sorted(m.name for m in agent.get_active_modes())
+        assert "editing" in initial_mode_names
+        assert "interactive" in initial_mode_names
+
+        # Switch to planning mode
+        agent.set_modes(["planning", "interactive"])
+
+        new_mode_names = sorted(m.name for m in agent.get_active_modes())
+        assert "planning" in new_mode_names
+        assert "interactive" in new_mode_names
+        assert "editing" not in new_mode_names
+
+    def test_set_modes_overrides_config_defaults(self) -> None:
+        """Test that set_modes takes precedence over config defaults."""
+        config = SerenaConfig(gui_log_window=False, web_dashboard=False, log_level=logging.ERROR)
+        config.default_modes = ["editing", "interactive"]
+        agent = SerenaAgent(serena_config=config)
+
+        # Verify config defaults are active
+        initial_mode_names = [m.name for m in agent.get_active_modes()]
+        assert "editing" in initial_mode_names
+
+        # Switch modes — should override config defaults
+        agent.set_modes(["planning", "one-shot"])
+
+        new_mode_names = [m.name for m in agent.get_active_modes()]
+        assert "planning" in new_mode_names
+        assert "one-shot" in new_mode_names
+        assert "editing" not in new_mode_names
+
+    def test_set_modes_persists_after_repeated_calls(self) -> None:
+        """Test that set_modes result persists (modes don't revert)."""
+        agent = self._create_agent(modes=ModeSelectionDefinition(default_modes=["editing"]))
+
+        agent.set_modes(["planning"])
+        mode_names_1 = [m.name for m in agent.get_active_modes()]
+        assert "planning" in mode_names_1
+
+        # Call get_active_modes again — should still be planning
+        mode_names_2 = [m.name for m in agent.get_active_modes()]
+        assert mode_names_1 == mode_names_2
+
+    def test_set_modes_can_switch_back(self) -> None:
+        """Test that modes can be switched back to original after switching away."""
+        agent = self._create_agent(modes=ModeSelectionDefinition(default_modes=["editing", "interactive"]))
+
+        # Switch away
+        agent.set_modes(["planning", "one-shot"])
+        assert "planning" in [m.name for m in agent.get_active_modes()]
+
+        # Switch back
+        agent.set_modes(["editing", "interactive"])
+        mode_names = [m.name for m in agent.get_active_modes()]
+        assert "editing" in mode_names
+        assert "interactive" in mode_names
+        assert "planning" not in mode_names