Specifically, make-deploy-one.sh is being too conservative about which jar files it's picking up. It should probably be more brutal and just grab everything matching "${PROJECT}-${VERSION}-*.jar".
Will start work on this immediately.
Should be fixed in jogamp-scripting 7f28cc15004e143f77f7b90f8e543c16f84dcff0.
I've ended up actually being more strict with it in some respects. The initial make-copy-jars.sh pass uses a list of atomics given in make-projects.txt and writes out a manifest file of every jar file included. The make-deploy-one.sh script then reads this manifest and uploads everything on it (as opposed to redoing some of the work of make-copy-jars.sh as it did before).
Just waiting for the next aggregated build to check that everything is actually present.