More examples and documentation

[rwest]

I think it'd be good to provide more example files, especially as we have so many options now. Things to show:

• how to do oxidation right
  • Oj-Oj
  • primary libraries
• how to do things fast
  • something without pressure dependence (or with MSC)
• how to use prior knowledge
  • primary reaction libraries
  • seed mechanisms
  • primary thermo libraries
• how to keep things manageable
  • pruning
  • forbidden structures
  • atom count and radical limits

Thoughts?

[gmagoon]

partially addressed by 5d1fcff087385c263053f36c2f3ec523b4fe7e86

[mrharper]

I've been adding bits and pieces over the last few days ... though they don't address any of the specific issues listed here.

[rwest]

I have created a branch called documentation to keep our documentation work (which will involve many small commits) from making a confusing mess of our master branch. https://github.com/GreenGroup/RMG-Java/compare/master...documentation

To use it:

git fetch official
git checkout -b documentation official/documentation
<make wonderful changes in a series of commits>
git pull official documentation
(if someone else did something then optionally:
    git fetch official
    git rebase official/documentation
)
git push official documentation