Support overlayfs whiteouts on checkout

Support overlayfs whiteouts on checkout

Introduces an intermediate format for overlayfs storage, where
.wh-ostree. prefixed files will be converted into char 0:0
whiteout devices used by overlayfs to mark deletions across layers.

The CI scripts now uses a volume for the scratch directories
previously in /var/tmp otherwise we cannot create whiteout
devices into an overlayfs mounted filesystem.

Related-Issue: #2712