Probably you have seen a hidden file in all your directory structure called .keep and wondered what this file is for.
And here goes the answer (from Gentoo forums):
1. They prevent emerge’s autoclean option (which is enabled by default) from removing certain directories, even if they are empty. They are created by /usr/lib/portage/bin/ebuild.sh, which is part of portage, when a “keepdir” directive is included in an ebuild.
2. if you remove a software package from your system (emerge -C …), it’s possible that you remove all files from a directory. in such a situation that directory is removed. To prevent directories from beeing removed there are those “hidden” .keep files (hidden because they don’t match e.g. a ‘rm -f *’). They were created when you installed your system. additionally, some ebuild create such files.