cleaning & recontenting the file structure

[exaexa]

This shall close #42 .

Although the size of the PR looks super scary, not much has changed; most of the diff is just moving implementation parts around. Notably, some files were split into new parts of file structure:

• utils/ contains various misc functions that were bundled with model types and in base/utilities.jl
• mods/ now contains the "modifications" for models in FBA, categorized by the model they work on; I also separated out mods/generic.jl that work on anything
• io/show/ for prettyprinting implementations

Other than that, there are a few code changes, mainly regarding the construction of Reaction, Metabolite and Gene

• redundant constructors were removed and unified to work with new
• for constructors of more than 4 arguments we now enforce named arguments
• I simplified the model loading from .M and .json files to enjoy the fact that the structure is mutable
• I converted occurrences of the wildly popular but non-semantic Array{...,1} to Vector. (Type theory addendum: numbers in types should be avoided at all cost 😁)

One fixup that I packed on the way:

• CobraModel was renamed to StandardModel also in docs (this will collide with Marvin's PR but it should automerge without much trouble)

[exaexa]

The comments are resolved separately in #79, merge order ideally #79 → #78 → master.

[exaexa]

🎉 🍾