sysroot: Handle deleting directories in /etc

We need to use the full shutil_rm_rf() in order to actually delete
complete directories.

Test suite code based on a patch from Sjoerd Simons <sjored@luon.net>

https://bugzilla.gnome.org/show_bug.cgi?id=710097
trivial: Don't include config.h in headers

This should be included by each .c file.  This fixes using libostree
from a "plain" project without config.h.