In Rails 4, your app's bin/ directory contains executables that are versioned like any other source code, rather than stubs that are generated on demand.
Here's how to upgrade:
bundle config --delete bin # Turn off Bundler's stub generator
rake rails:update:bin # Use the new Rails 4 executables
git add bin # Add bin/ to source control
You may need to remove bin/ from your .gitignore as well.
When you install a gem whose executable you want to use in your app, generate it and add it to source control:
bundle binstubs some-gem-name
git add bin/new-executable