Видимо никак
http://linux.die.net/man/1/patchЦитата
Caveats Context diffs cannot reliably represent the creation or deletion of empty files, empty directories, or special files such as symbolic links. Nor can they represent changes to file metadata like ownership, permissions, or whether one file is a hard link to another. If changes like these are also required, separate instructions (e.g. a shell script) to accomplish them should accompany the patch.
Как обходной путь, можно скрипты вызывать не './foo.sh' а '$(SHELL) ./foo.sh'