Set Gem.sources directly for source in gem.deps.rb

There isn't a provision for setting sources for a particular resolve set
at this time.  This means we can't override the sources for just this
one resolution.

Instead, we set the sources directly on Gem.sources and use them.  Since
multiple gem dependencies files are typically not used in the same
process this should not be an issue for time being.
Include gems regardless of groups

Groups are opt-out, not opt-in.  This matches bundler behavior.
Add without-group filtering for gem dependencies

Now the gem dependencies APIs is able to exclude dependencies by naming
their groups.
Add --without option to install

Now a Gemfile can be installed without groups.  Unlike bundler, you must
comma-separate the arguments to --without.  Perhaps bundler rolled its
own option parser?