add builder dependency to assist in bundling

Bundler was getting confused trying to resolve the builder dependency,
so we specify a dependency even though there is no direct dependency.
This can be removed when the issue is fixed in bundler or if we no
longer depend on any other gems that depend on builder.
update yard dependency

No reason to lock to ~> 0.8.5.2.
update rdoc dependency

No reason to lock to ~> 3.12.2.
update rdiscount dependency

No reason to lock to ~> 2.0.7.