Add discussion pages

[cbizon]

I've added a discussion section to the user guide. We need pages on
-Genetic Condition and why we did it
-Allele/Haplotype/Genotype Contextual/Canonical AlleleModel/VMC
-DomainEntities & the different ways to use them (just IRI, IRI+name, type, userlable)
-How to code a benign variant
-How to use the NOT qualifier

[cbizon]

See #60 for useful discussion the benign question.

[cbizon]

I've added several pages under User/Discussion. I'm going to hand this ticket over to others to read and revise the text.

[bpow]

I've reviewed an made edits to these-- except for DomainEntity since that is part of the discussion for #185.