Update to Reaction context

[dpvc]

This is a PR that includes a bunch of new features that I had in the wings but was waiting for some feedback from the folks I made the changes for (which never came). In light of openwebwork/mathquill#41, I thought I'd fix that problem, and include these other changes as well.

The changes here are to:

• Tighten syntactic checks,
• combine adjacent equal elements,
• add conversion to molecular form,
• allow comparisons based on molecular forms,
• and better handling of charges.

See the changes to the comments (in particular the new large section on molecular form). There are a bunch of new flags to control how the checking is performed.

The new section in the Close() method of the context::Reaction package is the part that fixes the parentheses around charges.

Some methods that are common to multiple objects have been moved into a new context::Reaction::common package, and there is new data stored about the elements in a compound that is used to manage the molecular form. Most of the rest is new methods used for computing the molecular forms.

[sfiedle1]

The following warning appears when running the MWE given in openwebwork/mathquill#41:

Argument "type" isn't numeric in subtraction (-) at line 874 of [PG]/macros/contexts/contextReaction.pl

Without sinking into the code, this warning can be suppressed if "$other -type" in line 874 is changed to "$other ->type".

[dpvc]

Thanks @sfiedle1, I'm not sure how that got messed up. I've added a commit to fix it.