You might want to check here.
https://code.google.com/p/rowboat/
Gerald
Wish I could help. I am the hardware team. You need to hear from the SW folks.
They have an IRC and a mailing list you might check.
Gerald
the mailing list being the very one we are just using
Note that the rowboat project does not support the Black (yet).
for special APIs to use the peripherals of the Beaglebone, I dont know how much rowboat supports, this might be an area where you would need to involve yourself more deeply. On the other hand, all the C APIs that exist can also be used from the Java world via JNI.