You can use git stash - if something goes wrong, you can still revert from the stash. Similar to some other answer here, but this one also removes all unstaged files and also all unstaged deletes:
git add .
git stash
if you check that everything is OK, throw the stash away:
git stash drop
The answer from Bilal Maqsood with git clean
also worked for me, but with the stash I have more control - if I do sth accidentally, I can still get my changes back
UPDATE
I think there is 1 more change (don't know why this worked for me before):
git add . -A
instead of git add .
without the -A
the removed files will not be staged