The best way to list these file is using git status --porcelain.
For example:
git status --porcelain | awk 'match($1, "D"){print $2}'
shows you the tracked files which have been deleted from the local copy. You can delete all these files by appending an appropriate command to the pipe:
git status --porcelain | awk 'match($1, "D"){print $2}' | xargs git rm