When a file is removed from the project (by right click on the filename -> Remove File) a confirmation dialog appears. This dialog allows to delete the file permanently.

If this dialog is accepted with "delete file permanently" and the file is under version control, a second dialog appears, asking if the file should be removed from the VCS.

My first suggestion was to combine these questions into one dialog with a radio selection:

• Remove from project only but keep local file
• Delete local file but keep in version control
• Delete local file and remove from version control

But while thinking about it, I wonder which advantage point two brings. Even if the file is removed from the VCS, this transaction still needs to be committed and can therefore be undone.