Make bundling binstubs optional to match with rails 4.0 and Bundler 1.3.5

To sync up Capistrano 3.0 with Rails 4.0 and Bundler 1.3.5, this change removes the default --binstubs parameter on the bundle command, and adds an optional parameter ( boolean  :bundle_binstubs ) that can be added to the deploy.rb if the project requires it.

The defaults for the linked_dirs folders and related tests have also been updated to remove this as a shared dir.

As per rails 4.0 recommendations, the following changes should be made to a rails 3.0 app that has been converted to 4.0:

1. remove /bin from the .gitignore
2. run 'bundle config --delete bin' to remove from the local bundle config
3. run 'bundle binstubs <gem name>' for each gem that has a binary component
4. add each file in /bin to the git repository