The second item, com.serotonin.m2m2.Common.databaseProxy.newPointValueDao()
is actually a specific call into the Java code. The com.serotonin.m2m2 is the package path to the class Common, which has member variable databaseProxy. The returned object is still a native Java object. There isn't documentation for this because it simply wouldn't be feasible. The code is open source, it's about the best we can do for direct references to the Java code.