[1D] Change 'save' behavior to avoid endlessly appending solutions

Instead of changing the solution 'id' provided by the user to avoid
duplicates, replace the solution with the same id.
Deprecate XML_Node::operator()
[Transport] Check for invalid 'geometry' flags

For those cases where the number of atoms in a molecule precludes certain
geometries, check to make sure that that the geometry flag is set
appropriately.
[MixMaster] Fix crash when using Tcl 8.6

Tcl/Tk changed some operations which previously resulted in undefined behavior
into errors, including one case that occurred when updating the "Mixtures" menu
in MixMaster.

MixMaster now modifies the existing Menu when adding an item, rather than
completely regenerating it, which avoids this problem.

Fixes Issue 235.