you can go for a hybrid solution. i.e. using skeleton animation create jPCT's regular mesh based key frame animations on the fly and use that afterwards. this will increase performance but you may hit memory limit (depends on number/length of your animations)

but of course you should first create the list if it's null

map = Map<Integer, List<Integer>>();
for (b: boneRefs) {
  list = map.get(b.vertexIndexReference);
  if (list == null) {
    list = new ArrayList<Integer>();
    map.put(b.vertexIndexReference, list);
  }
  list.add(b.boneIndexReference);
}

you cant do that in a single iteration IMHO.*

first iterate over boneRefs to collect vertex-bone relations

map = Map<Integer, List<Integer>>();
for (b: boneRefs) {
  map.get(b.vertexIndexReference).add(b.boneIndexReference);
}

then loop over your map to place into jointIndices array. sth like this

for (e : map.entrySet) {
  count = 0;
  for (index : e.value) {
    jointIndices[e.key][count++] = index;
  }
}

hope this helps
r a f t

(*) actually you can but will be ugly

MAX_JOINTS_PER_VERTEX = 4

jointIndices is a [mesh size][MAX_JOINTS_PER_VERTEX] short array, describing which joints in skeleton is affecting each vertex.

weights is a [mesh size][MAX_JOINTS_PER_VERTEX] float array, describing how much each vertex is affected by corresponding joint in skeleton. if weight is zero, no calculation is done and corresponding jointIndex is irrelevant.

to get the rotation quat:

new Quaternion(SkeletonPose.getLocal(<index>))
and for sure that means, SkeletonPose.getLocal(<index>) actually contains the rotation information.

Joint.getBindPose()/getInverseBindPose() gives you information about the bind pose, not current translation/rotation.

you need pull that information from the matrices in SkeletonPose

first make sure you didnt call AnimatedGroup/Animated3D.setAutoApplyAnimation(false), otherwsie you need to call AnimatedGroup/Animated3D.applyAnimation manually each frame.

looking at your code, you dont update quat2 and quat3 but update quat 3 times.

and also try adding some translation to your joint, rotations sometimes behave very unexpectedly.

np, it happens