Use pure Ruby Markdown parser for JRuby compatibility

When generating documentation, use kramdown instead of rdiscount to
parse Markdown. It is implemented in pure Ruby (no C extensions) so it
is compatible with JRuby and other Ruby interpreters. It is somewhat
slower on MRI but still reasonably fast.
Update aruba development dependency to '~> 0.5.0'
Use MultiJSON for JSON parsing

Closes #359.
Update gem tasks to use MultiJSON
Alphabetize dependencies within groups