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!
There is some code in place now to create wells for the no-deck case,
but since it does not work correctly yet, the simulator intercepts this
and throws.
