add tests, fix implementation

pkgs/dart_tooling_mcp_server/lib/src/utils/cli_utils.dart

@@ -72,6 +72,7 @@ Future<CallToolResult> runCommandInRoots(
                 'registered project roots:\n\n${knownRoots.join('\n')}',
           ),
         ],
+        isError: true,
       );
     }
 
@@ -92,9 +93,13 @@ Future<CallToolResult> runCommandInRoots(
 
     final commandWithPaths = List.of(command);
     final paths =
-        (rootConfig[ParameterNames.paths] as List?)?.cast<String>() ??
+        (rootConfig[ParameterNames.paths] as List?)?.cast<String>().map(
+          (path) => rootUri.resolve(path).toString(),
+        ) ??
         defaultPaths;
-    final invalidPaths = paths.where((path) => !p.isWithin(rootUri.path, path));
+    final invalidPaths = paths.where(
+      (path) => !p.isWithin(rootUri.toString(), path),
+    );
     if (invalidPaths.isNotEmpty) {
       return CallToolResult(
         content: [

pkgs/dart_tooling_mcp_server/test/tools/dart_cli_test.dart

@@ -55,7 +55,7 @@ void main() {
       );
       final result = await testHarness.callToolWithRetry(request);
 
-      // Verify the command was sent to the process maanger without error.
+      // Verify the command was sent to the process manager without error.
       expect(result.isError, isNot(true));
       expect(testProcessManager.commandsRan, [
         ['dart', 'fix', '--apply'],
@@ -73,7 +73,7 @@ void main() {
       );
       final result = await testHarness.callToolWithRetry(request);
 
-      // Verify the command was sent to the process maanger without error.
+      // Verify the command was sent to the process manager without error.
       expect(result.isError, isNot(true));
       expect(testProcessManager.commandsRan, [
         ['dart', 'format', '.'],
@@ -94,7 +94,7 @@ void main() {
       );
       final result = await testHarness.callToolWithRetry(request);
 
-      // Verify the command was sent to the process maanger without error.
+      // Verify the command was sent to the process manager without error.
       expect(result.isError, isNot(true));
       expect(testProcessManager.commandsRan, [
         ['dart', 'format', 'foo.dart', 'bar.dart'],

pkgs/dart_tooling_mcp_server/test/utils/cli_utils_test.dart

@@ -0,0 +1,82 @@
+// Copyright (c) 2025, the Dart project authors.  Please see the AUTHORS file
+// for details. All rights reserved. Use of this source code is governed by a
+// BSD-style license that can be found in the LICENSE file.
+
+import 'package:dart_mcp/server.dart';
+import 'package:dart_tooling_mcp_server/src/utils/cli_utils.dart';
+import 'package:dart_tooling_mcp_server/src/utils/constants.dart';
+import 'package:process/process.dart';
+import 'package:test/fake.dart';
+import 'package:test/test.dart';
+
+void main() {
+  final processManager = FakeProcessManager();
+
+  test('cannot run commands with roots outside of known roots', () async {
+    final result = await runCommandInRoots(
+      CallToolRequest(
+        name: 'foo',
+        arguments: {
+          ParameterNames.roots: [
+            {ParameterNames.root: 'file:///bar/'},
+          ],
+        },
+      ),
+      command: ['fake'],
+      commandDescription: '',
+      processManager: processManager,
+      knownRoots: [Root(uri: 'file:///foo/')],
+    );
+    expect(result.isError, isTrue);
+    expect(
+      result.content.single,
+      isA<TextContent>().having(
+        (t) => t.text,
+        'text',
+        contains('Invalid root file:///bar/'),
+      ),
+    );
+  });
+
+  test('cannot run commands with paths outside of known roots', () async {
+    final result = await runCommandInRoots(
+      CallToolRequest(
+        name: 'foo',
+        arguments: {
+          ParameterNames.roots: [
+            {
+              ParameterNames.root: 'file:///foo/',
+              ParameterNames.paths: [
+                'file:///bar/',
+                '../baz/',
+                'zip/../../zap/',
+                'ok.dart',
+              ],
+            },
+          ],
+        },
+      ),
+      command: ['fake'],
+      commandDescription: '',
+      processManager: processManager,
+      knownRoots: [Root(uri: 'file:///foo/')],
+    );
+    expect(result.isError, isTrue);
+    expect(
+      result.content.single,
+      isA<TextContent>().having(
+        (t) => t.text,
+        'text',
+        allOf(
+          contains('Paths are not allowed to escape their project root'),
+          contains('bar/'),
+          contains('baz/'),
+          contains('zap/'),
+          isNot(contains('ok.dart')),
+        ),
+      ),
+    );
+  });
+}
+
+class FakeProcessManager extends Fake implements ProcessManager {}