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

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.

dracut/99setup-root/initrd-setup-root

@@ -147,6 +147,14 @@ mkdir -p /sysroot/etc
 if [ ! -e "/sysroot/etc/.no-dup-update" ]; then
   walksysroot /etc overlaycleanup
 fi
+# Also, remove any user-created whiteouts for files that have a tmpfiles
+# rule that normally would recreate them (we use the lowerdir for that).
+while IFS="" read -r entry ; do
+  entry="/sysroot${entry}"
+  if [ -c "${entry}" ] && [ "$(stat --printf='%Hr %Lr\n' "${entry}")" = "0 0" ]; then
+    rm "${entry}" || true
+  fi
+done < /sysroot/usr/share/flatcar/etc-no-whiteouts
 
 # Set up overlay mount for /etc (as long as we can't use syscfg for that)
 mkdir -p /sysroot/.etc-work