Exclude submodules from modified_files

The command to extract modified files is currently `git diff --cached --name-only --diff-filter=ACM`, which includes any added submodule directories. This confuses eg. the whitespace checker, which tries to do `git diff` on them producing messages such as `bad object :libs/iberty`. I don't think having submodule directories in the list is useful, as there's no content to check there anyway, so this patch removes them.