initrd-setup-root: Clean up whiteout entries for files to be recreated

[pothos]

The removal of files in the overlay present in the lowerdir creates whiteout entries that mask the lowerdir entries. For those files that have a tmpfile rule for creation, a reboot would cause the file to be created in the upperdir, meaning this file is not updated from the lowerdir when it changes. In addition we have filtered out some tmpfile rules that caused upcopies (symlinks and directories) which meant that removing the /etc/resolv.conf symlink didn't bring it back after reboot. To make files from the lowerdir show up if they have a tmpfile rule that normally would recreate them we keep a list of whiteout entries that we clean up on boot. This also prevents freezing files because systemd-tmpfiles does not need to recreate them in the upperdir.

How to use

Backport to Stable

Testing done

Removal of /etc/resolv.conf and reboot brings it back.

Note that not all files have a tmpfiles rule, e.g., sshd_config has not. We could identify files like that which need to exist for a working system by running rm -rf /etc/* and rebooting.
This is different from the removal of /etc contents after umount /etc which works without a problem and brings all files back.

• Changelog entries added in the respective changelog/ directory (user-facing change, bug fix, security fix, update)
• Inspected CI output for image differences: /boot and /usr size, packages, list files for any missing binaries, kernel modules, config files, kernel modules, etc.

[pothos]

Tested with flatcar/mantle#488