Bundler should always install gems somewhere within the application directory

[crowbot]

At the moment, we only use the --deployment flag when calling bundler for a non-staging site. This means that for staging sites, gems are installed in the system path. For avoiding our own server management headaches, we should always install the gems in a path local to the application. Additionally, I suspect this might also resolve #611, as it is the reason why bundler is using sudo to install rake.

Note: this needs to work for capistrano-based deploys.