The existing tmpfile logic took care of folders that the ebuild keepdir
directive wanted to exist on the OS. However, files and symlinks were
not created, causing them to be missing if we didn't explicitly modify
the ebuild files in coreos-overlay to find a solution with tmpfiles or
patching the paths to /usr.
Add logic to create missing files and symlinks through tmpfile
directives and preserve any directory, not only the ones with the
keepdir ebuild directive. Also remove any state from the rootfs to make
sure that we don't rely on it when testing our images before the
release. To create the files the final /etc folder is moved to
/usr/share/flatcar/etc and in the future this can be used for a better
logic that could take care of updating files the user didn't modify,
deleting those that aren't needed anymore, and even reconciling changed
files through a 3-way merge, instead of using simple tmpfile logic.