As I said in my comment, bundle
with the --deployment
flag (as Capistrano does) installs gems into a your_app/shared/bundle
. One of the reasons for this isolation and location is because the user you're deploying with may not have access to install gems to a system location, and more reasons described here (under the Deploying Your Application heading).
I believe there are ways to force bundler to use the system gems but I don't have any first hand experience of it; see here.