v3: Should not be using "bundler --binstubs"

[archseer]

See https://gist.github.com/chrismo/5043420. This is why you were having problems with the binstubs overwriting the rails default ones.

I think the script/bootstrap should be modified to generate binstubs only for a select list of gems here.

Anyone that has already bootstrapped the project should manually edit their .bundle/config, because bundler remembers the --binstubs option and generates binstubs again any time you run bundler again.

Since we generate the binstubs as a part of the bootstrapping process, I think we can remove them from version control. They'll get regenerated any time one runs script/bootstrap anyway.

[archseer]

(We actually don't seem to be using much of the binstubs anyway, for instance bin/unicorn could replace bundle exec unicorn et cetera)