Sometimes when comparing two directories, a file may exist in one directory but not the other. If you give diff the --new-file (-N) option, or if you supply an old or new file that is named /dev/null or is empty and is dated the Epoch (1970-01-01 00:00:00 UTC), diff outputs a patch that adds or deletes the contents of this file. When given such a patch, patch normally creates a new file or removes the old file. However, when conforming to POSIX (see patch and POSIX), patch does not remove the old file, but leaves it empty. The --remove-empty-files (-E) option causes patch to remove output files that are empty after applying a patch, even if the patch does not appear to be one that removed the file.
If the patch appears to create a file that already exists, patch asks for confirmation before applying the patch.