So git pull merges by default, when it should really rebase. You can ask it to rebase instead, but it still won't touch anything other than the currently checked-out branch. If you're tracking a bunch of remote branches, you'll get non-fast-forward complaints next time you push.
Solve it once and for all:
git-up might mess up your branches, or set your chest hair on fire, or be racist to your cat, I don't know. It works for me.
git-up has a few configuration options, which use git's configuration system. Each can be set either globally or per-project. To set an option globally, append the --global flag to git config, which you can run anywhere:
git config --global git-up.bundler.check true
To set it within a project, run the command inside that project's directory and omit the --global flag:
cd myproject
git config git-up.bundler.check true
If set to true, git-up will check your app for any new bundled gems and suggest a bundle install if necessary.
It slows the process down slightly, and therefore defaults to false.
If you're even lazier, you can tell git-up to run bundle install for you if it finds missing gems. Make sure git-up.bundler.check is also set to true or it won't do anything.
By default, git-up will append the --prune flag to the git fetch command if your git version supports it (1.6.6 or greater), telling it to delete any branches which no longer exist on the remote. Set this option to false to disable it.