Fix dangling registered project poisoning project lookup/activation

A registered project whose root directory was deleted (e.g. a removed git
worktree) would raise FileNotFoundError from RegisteredProject.matches_root_path
(via Path.samefile). Because get_registered_project iterates matches_root_path
over every registered project, one dangling entry aborted activation of all
other, valid projects until an MCP server restart.

matches_root_path now treats a non-existent directory as a non-match instead of
letting the filesystem error propagate.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

CHANGELOG.md

@@ -20,6 +20,8 @@ Status of the `main` branch. Changes prior to the next official version change w
   - Improve quoting/escaping of arguments in shell executions on Windows (via `oslex` dependency)
   - Add tool parameter alias support, adding `name_path` as an alias for `name_path_pattern` in `find_symbol` tools
   - Make tool call errors surface explicitly as errors at the MCP protocol level
+  - Fix: a registered project whose root directory was deleted while Serena was already running could break
+    `activate_project`/project lookup, raising `FileNotFoundError` in `RegisteredProject.matches_root_path`
 
 * Language Servers:
   - `typescript_vts`: Add `initialization_options` setting in `ls_specific_settings.typescript_vts`.

src/serena/config/serena_config.py

@@ -705,9 +705,14 @@ class RegisteredProject(ToStringMixin):
         Check if the given path matches the project root path.
 
         :param path: the path to check
-        :return: True if the path matches the project root, False otherwise
+        :return: True if the path matches the project root, False otherwise (including the case
+            where this project's root directory no longer exists, e.g. a removed git worktree)
         """
-        return self.project_root.samefile(Path(path).resolve())
+        try:
+            return self.project_root.samefile(Path(path).resolve())
+        except OSError:
+            # typically raised if the path does not exist (e.g., a removed git worktree)
+            return False
 
     def get_project_instance(self, serena_config: "SerenaConfig") -> "Project":
         """

test/serena/config/test_serena_config.py

@@ -569,6 +569,49 @@ class TestSerenaConfigFromConfigFileRobustness:
         )
 
 
+class TestGetRegisteredProjectWithDanglingProject:
+    """A registered project whose root directory was deleted (e.g. a removed git
+    worktree) must not break lookup/activation of other, valid projects.
+
+    Reproduces the bug where ``get_registered_project`` iterates over every
+    registered project and ``RegisteredProject.matches_root_path`` raises
+    ``FileNotFoundError`` for the dangling project, aborting the whole lookup.
+    """
+
+    def setup_method(self):
+        self.test_dir = Path(tempfile.mkdtemp())
+
+    def teardown_method(self):
+        shutil.rmtree(self.test_dir, ignore_errors=True)
+
+    def _make_project_dir(self, name: str) -> Path:
+        project_dir = self.test_dir / name
+        (project_dir / SERENA_MANAGED_DIR_NAME).mkdir(parents=True)
+        (project_dir / SERENA_MANAGED_DIR_NAME / "project.yml").write_text(f'project_name: "{name}"\nlanguages: ["python"]\n')
+        return project_dir
+
+    def test_dangling_project_does_not_break_lookup_of_valid_project(self):
+        config = create_default_serena_config()
+        dangling_dir = self._make_project_dir("dangling_project")
+        valid_dir = self._make_project_dir("valid_project")
+
+        # Register the dangling project FIRST so the path-matching loop hits the
+        # deleted directory before reaching the valid project.
+        config.projects = [
+            RegisteredProject.from_project_root(dangling_dir, serena_config=config),
+            RegisteredProject.from_project_root(valid_dir, serena_config=config),
+        ]
+
+        # Delete the dangling project's directory out from under Serena.
+        shutil.rmtree(dangling_dir)
+
+        # Looking up the valid project by path must succeed, not raise
+        # FileNotFoundError on the deleted dangling project's path.
+        result = config.get_registered_project(str(valid_dir))
+        assert result is not None
+        assert result.project_name == "valid_project"
+
+
 class TestMemoriesManagerCustomPath:
     """Tests for MemoriesManager with a custom serena data folder."""