It got past the important parts of the script, but you’re having a network issue as @mhall119 pointed out. These types of issues should not normally cause problems with the system (I don’t think it’s what caused you to get into this state), but it does cause a problem for this script, which is trying to download missing files. There are 2 issues with you’re repo indicated by these messages:
Marking commits with missing objects as partial in /sysroot/ostree/repo
Commit 8c30669098ec948fa948aee79e17441268d169542e7d39ea46d06ebc0f6d0f7a already marked as partial
Commit 544227a635b16b31833ee446661a8c108d364e9c8909748848f3c937eaef842f already marked as partial
That means that some app/runtime/os is missing files in the repository. What happens next is that one of these tries to be updated to get the missing files:
Pulling 8c30669098ec948fa948aee79e17441268d169542e7d39ea46d06ebc0f6d0f7a commit from eos-sdk for runtime/com.endlessm.apps.Platform.Locale/x86_64/1
But then you hit the networking problems. You can just keep running this script until it succeeds, though. It will just pick up where it left off.
Thanks very much for the feedback. I’ve never had a system with these issues, so it’s been a little hard to figure out how to fix them 
If you don’t mind, can you run the following command:
for ref in `ostree refs`; do rev=`ostree rev-parse $ref`; echo $ref $rev; done
You can just paste the output in your reply. Thanks!
