Currently when you click an error at project root level in PROBLEMS view, it will throw some error saying Unable to open 'project': File is a directory.

This error is like a bug. When the problems are showed in the PROBLEMS view, the user will expect to open the resource and able to fix it. For the Java language server, the closest project configuration resource file is .classpath, however it's apparently not friendly for user to edit it manually. One idea is the Java language server provides a special web view to show the project structure (such as build path).