Removed 'repo' object from refs page
References are entered by hand now

This lets us discontinue usingin Jekyll Scholar, which is a pain to get
working
Removed bib files, plugin files, took jekyll scholar out of config
deleted cruft, and outdated flags
Github overrides "safe" so lets set it to match
user rdiscount to parse markdown

old versions of Maruku (1.6.0 which is the last one gem will install on
os x) doesn't like parseing '_' and '*' correctly, rdiscount works fine
though
worked on webpage readme