[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/create_all_plugins_app_command_test.dart

@@ -30,7 +30,6 @@ void main() {
 
       final CreateAllPluginsAppCommand command = CreateAllPluginsAppCommand(
         packagesDir,
-        fileSystem,
         pluginsRoot: testRoot,
       );
       appDir = command.appDirectory;