avoiding duplicate setEAtom and updateMask in AnnotatedGroundProgram::initialize
structural and readability improvements
fixed assertion
making outputAtoms a bitset, adding some comments
formatting complicated condition
more comments
replacing auxInputTuples by auxInputMask

this improves scalability of marking such facts (and ensures the set property)
this simplifies the usage of aux input tuples in the model generators
this prepares for a different approach to matchOutputAtom