The most severe change probably is the removal of the AutoDiff
debugging helper functions which were useful from within a debugger
but unfortunately had to rely on a presumed linker bug in order not to
be removed in the final binary.
Also, some private attributes were unused. These have been removed and
the constructors of their respective classes have been adapted. Once
their intended functionality is actually implemented, they should be
brought back on an as-needed basis.
Thanks to @bska for the review!
Code is now functionally complete apart from lacking miscibility,
not writing to all promised output variables and not writing the
promised output to disk. Initial testing has been unsuccessful,
so there are bugs in the code.
