It appears that the Modeler is trying to add a file to a directory that is 'scheduled for deletion', i.e. still exists on disk, but will be deleted in the next commit. I'm not sure how this happened, but it could have something to do with updating the CommunityCommons module.
The Modeler should handle this better (I'll put this on our to-do list), but for now you can fix it in one of two ways:
Delete the project directory on disk and do a fresh download from the Team Server. Please note that when doing this, you will lose all local changes that you made since the last time you committed.
To fix the existing project directory without deleting it, you could try the following steps:
Now the new CommunityCommons module with all included Java files should be in the Team Server.
Please let me know if this solves your problem.
Great answer, it worked for me!