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

@@ -66,6 +66,16 @@ if [ -s /sysroot/selective-os-reset ]; then
   rm -f /sysroot/etc/machine-id
 fi
 
+# Remove any user-created whiteouts for files that have a tmpfiles
+# rule which normally would recreate them (we use the lowerdir for that).
+while IFS="" read -r entry ; do
+  entry="/sysroot${entry}"
+  # The -c check for character devs also guards against empty strings and nonexisting files
+  if [ -c "${entry}" ] && [ "$(stat --printf='%Hr %Lr\n' "${entry}")" = "0 0" ]; then
+    rm "${entry}" || true
+  fi
+done < /sysroot/usr/share/flatcar/etc-no-whiteouts
+
 # This creates the modifiable users/groups in /sysroot/etc,
 # initializing the shadow database in the process. This needs to
 # happen early, so systemd-tmpfiles can read the user info from