Allow valid permutations of molecules

[sjd210]

Allows for permutations of molecules to be accepted when the allowPermutations flag is set (off by default)
e.g. CH3(CH2)8CH3 or H22C10 for C10H22 and vice-versa

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NOTE: Only allows for Compound permutations of a Compound, so representing an entire Compound as a Bracket e.g. (C5H11)2 or as a Term with a different coefficient e.g. 2 C5H11 will not work.

The Compound can, however, be in any context such as within a Term and/or Statement.
e.g. CH3(CH2)8CH3 -> C8H18 + C2H4

Other changes would require a grammar rewrite, so can be handled later if wanted.

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Also fixes atomCount for Expressions by keeping a separate atomTermCount and atomBracketCount to get correctly multiplied by coefficients - rather than multiplying the entire aggregate count.

This breaks many of the tests in Chemistry.test.ts, but the tests were based on the incorrect previous counting system so this is okay. I will make a card to fix these at some point later.

[skyepurchase]

Looks good and nice to see a new feature being added by someone else! Not my initial thought process on how to solve the issue but I think definitely slicker.

It's a shame that atom counting was not as straight forward as I initially assumed.

I don't have time to properly test this so will leave it for proper code review (maybe someone else can learn my eccentric checker) but from the perspective of understanding how the checker works this appears sound.

[skyepurchase]

The only other request I would have is to move the tagging of Elements and Compounds as bracketed from this checker to the flatten function which probably needs a rename. This takes the suboptimal AST from the parser and makes it a little more checker friendly so seems sensible to add this AST addition there.

Potentially rename it augment? Though it originally just flattened the linked-list style AST lists to javascript arrays.

[sjd210]

This set of PRs now also covers a change to recognising matching bracket types, adds/re-prioritises default checker feedback, and adds some better server logging for the sake of being able to diagnose future problems.