[flutter_plugin_tools] Simplify filesystem usage (#4014)

- Replaces most explicit use of `fileSystem` with path construction using the `child*` utility methods
- Removes explicit passing of a filesystem to the commands; we're already passing a `Directory` for the
  root where the tool operates, and we should never be using a different filesystem than that directory's
  filesystem, so passing it was both redundant, and a potential source of test bugs.

script/tool/test/java_test_command_test.dart

@@ -17,9 +17,8 @@ void main() {
 
     setUp(() {
       initializeFakePackages();
-      final JavaTestCommand command = JavaTestCommand(
-          mockPackagesDir, mockFileSystem,
-          processRunner: processRunner);
+      final JavaTestCommand command =
+          JavaTestCommand(mockPackagesDir, processRunner: processRunner);
 
       runner =
           CommandRunner<void>('java_test_test', 'Test for $JavaTestCommand');