Let me put that line by line :)

1. find the content referenced by $ATOMICDEST in that patch
2. rm -rf it
3. mkdir $ATOMICDEST
4. ostree init --repo=$ATOMICDEST --mode=archive-z2

Which I think with the patch applied can be simplified to:

1. rm -rf $ATOMICDEST (which from lmacken I believe to be /mnt/fedora_koji/koji/mash/atomic/21/)
2. rerun the script or at least that part of it

the old repo has been removed and a new one built
{{{
http://dl.fedoraproject.org/pub/fedora/linux/atomic/21/
}}}
contains what should be a complete repo and
{{{
http://koji.fedoraproject.org/koji/taskinfo?taskID=8118903
}}}
has an image being built from it