Update outline

[jharenza]

Purpose

This PR updates the outline and adds a few repository references to the methods

UPDATE: I also added many files which were part of the OpenPBTA manuscript repo, esp CI files and CONTRIBUTING, updated links to be specific to this repo, and added in the README links to the PDF and HTML webpage. I also pulled over the author list from the OpenPBTA repo - not in any particular order, and not inclusive.

Closes #6

Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.

Which areas should receive a particularly close look?

Is there anything that you want to discuss further?

I was trying to figure out how to get Appveyor Bot to comment on the PR after checks, but couldn't figure it out.

Is the pull request ready for review?

yes

Pull review checklist

Unless otherwise noted above, this PR will be considered ready for review when all four items have been checked.

• All changes to text follow "one sentence per line" [Manubot instructions]
• All citations follow the Manubot citation instructions
• All changes or additions to tables follow the Manubot table instructions
• All figures follow the Manubot figure instructions
• There are no new spelling errors identified by the Manubot spellchecker

Spellcheck Step

The dictionary used for spellchecking can be updated.
Edit the file in build/assets/custom-dictionary.txt by adding new entries to the end.
You do not need to change anything else.
However, if you want to update the first line to have an accurate count of words and you want to remove non-unique ones, run the following command from within build/assets on your favorite OS X or Linux machine:

(( len = $(awk '!a[$0]++' < custom-dictionary.txt | wc -l ) - 1 )); tmpfile="$(mktemp)"; echo "personal_ws-1.1 en $len utf-8" > $tmpfile; tail -n +2 custom-dictionary.txt | awk '!a[$0]++' >> $tmpfile; mv $tmpfile custom-dictionary.txt

[jharenza]

Also closes #11

[jharenza]

@ewafula thanks for the comments, ready for re-review!

[ewafula]

Thank @jharenza, for updating. Now looks good to me.