Ok, so I found this thread, and using java from within the Defold app bundle instead of the standard one ran without issues if I removed the ext-dirs parameters.
This will give me the “Unable to create ManifestFile, hashing algorithm is not supported!” error (regardless of using the Defold or default Java), but most of the project will be built so after that running
I have the same issue. Archiving fails with ERROR level/level.collection:0 javax.vecmath.Vector3d.getX()D on java 1.8.0_144. Also tried with Defold’s java with no luck.