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

bash/ostree

@@ -249,6 +249,7 @@ _ostree_checkout() {
         --union-identical
         --user-mode -U
         --whiteouts
+        --process-passthrough-whiteouts
     "
 
     local options_with_args="