This is weird. You said that some of the apps won't respond to requests. What does that mean? Do those request make the server return a 404?
Restarting the "cluster" should sync the repositories. I am not exactly sure why so many copies of the application are found in /var/tmp. When the deployment is done, you should see nothing left over anywhere. The central repo is at domain-folder/applications and the copies are at all the instances e.g. managed-instance-machine/nodeagents/machine-name/instance-name/applications.
Can you file a bug with detailed instructions about how to reproduce it?
Thanks,
Kedar
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