How can I remove a file from Git within IntelliJ VCS?

In the terminal, use git rm --cached -r .idea/. This will remove the files from the GIT index, but leave the files locally.

To change a file from green (staged) to red (untracked) using Intellij:

1. Right click the file(s)
2. Hover over Git (the git pane will expand)
3. Click Rollback... (in older versions Revert)
4. Check that Delete local copies of added files is not checked and click the Rollback button

This will not delete the file, only unstage it (remove it from git's index).