ListTop.java is part of the community commons. I am more worried about the parent directory scheduled for deletion part. What did you delete in your project directory? Did you try to delete the javasource directory?
You might try exporting the changes you want to commit to a seperate directory and then download a fresh version of the model and redo all your changes.
Regards,
Ronald
I ran into a similar problem today and this solution worked wonders for me:
https://community.mendix.com/link/space/app-development/questions/4156