local_working_copy: on check out, skip entries conflicting with untracked dirs

This seems more consistent because file->directory conflicts are skipped.

lib/src/local_working_copy.rs

@@ -487,7 +487,7 @@ fn create_parent_dirs(
 }
 
 /// Removes existing file named `disk_path` if any. Returns `Ok(true)` if the
-/// file was there and got removed.
+/// file was there and got removed, meaning that new file can be safely created.
 ///
 /// If the existing file points to ".git" or ".jj", this function returns an
 /// error.
@@ -496,6 +496,8 @@ fn remove_old_file(disk_path: &Path) -> Result<bool, CheckoutError> {
     match fs::remove_file(disk_path) {
         Ok(()) => Ok(true),
         Err(err) if err.kind() == io::ErrorKind::NotFound => Ok(false),
+        // TODO: Use io::ErrorKind::IsADirectory if it gets stabilized
+        Err(_) if disk_path.symlink_metadata().is_ok_and(|m| m.is_dir()) => Ok(false),
         Err(err) => Err(CheckoutError::Other {
             message: format!("Failed to remove file {}", disk_path.display()),
             err: err.into(),
@@ -1550,9 +1552,9 @@ impl TreeState {
                 continue;
             };
             // If the path was present, check reserved path first and delete it.
-            let was_present = before.is_present() && remove_old_file(&disk_path)?;
+            let present_file_deleted = before.is_present() && remove_old_file(&disk_path)?;
             // If not, create temporary file to test the path validity.
-            if !was_present && !can_create_new_file(&disk_path)? {
+            if !present_file_deleted && !can_create_new_file(&disk_path)? {
                 changed_file_states.push((path, FileState::placeholder()));
                 stats.skipped_files += 1;
                 continue;

lib/tests/test_local_working_copy.rs

@@ -1242,6 +1242,13 @@ fn test_git_submodule() {
     // when we snapshot
     let new_tree = test_workspace.snapshot().unwrap();
     assert_eq!(new_tree.id(), tree_id2);
+
+    // Check out the empty tree, which shouldn't fail
+    let ws = &mut test_workspace.workspace;
+    let stats = ws
+        .check_out(repo.op_id().clone(), None, &store.root_commit())
+        .unwrap();
+    assert_eq!(stats.skipped_files, 1);
 }
 
 #[test]
@@ -1260,15 +1267,47 @@ fn test_check_out_existing_file_cannot_be_removed() {
     let ws = &mut test_workspace.workspace;
     ws.check_out(repo.op_id().clone(), None, &commit1).unwrap();
 
-    // Trigger IO error by replacing file with directory.
+    // Make the parent directory readonly.
+    let writable_dir_perm = workspace_root.symlink_metadata().unwrap().permissions();
+    let mut readonly_dir_perm = writable_dir_perm.clone();
+    readonly_dir_perm.set_readonly(true);
+
+    std::fs::set_permissions(&workspace_root, readonly_dir_perm).unwrap();
+    let result = ws.check_out(repo.op_id().clone(), None, &commit2);
+    std::fs::set_permissions(&workspace_root, writable_dir_perm).unwrap();
+
+    // TODO: find a way to trigger the error on Windows
+    if !cfg!(windows) {
+        assert_matches!(
+            result,
+            Err(CheckoutError::Other { message, .. }) if message.contains("Failed to remove")
+        );
+    }
+}
+
+#[test]
+fn test_check_out_existing_file_replaced_with_directory() {
+    let settings = testutils::user_settings();
+    let mut test_workspace = TestWorkspace::init(&settings);
+    let repo = &test_workspace.repo;
+    let workspace_root = test_workspace.workspace.workspace_root().to_owned();
+
+    let file_path = RepoPath::from_internal_string("file");
+    let tree1 = create_tree(repo, &[(file_path, "0")]);
+    let tree2 = create_tree(repo, &[(file_path, "1")]);
+    let commit1 = commit_with_tree(repo.store(), tree1.id());
+    let commit2 = commit_with_tree(repo.store(), tree2.id());
+
+    let ws = &mut test_workspace.workspace;
+    ws.check_out(repo.op_id().clone(), None, &commit1).unwrap();
+
     std::fs::remove_file(file_path.to_fs_path_unchecked(&workspace_root)).unwrap();
     std::fs::create_dir(file_path.to_fs_path_unchecked(&workspace_root)).unwrap();
 
-    let result = ws.check_out(repo.op_id().clone(), None, &commit2);
-    assert_matches!(
-        result,
-        Err(CheckoutError::Other { message, .. }) if message.contains("Failed to remove")
-    );
+    // Checkout doesn't fail, but the file should be skipped.
+    let stats = ws.check_out(repo.op_id().clone(), None, &commit2).unwrap();
+    assert_eq!(stats.skipped_files, 1);
+    assert!(file_path.to_fs_path_unchecked(&workspace_root).is_dir());
 }
 
 #[test]