Bundler is launched from your app's root directory so it makes sure all needed gems are present to get your app working.If for some reason you no longer need a gem you'll have to run the
gem uninstall gem_name
as you stated above.So every time you run bundler it'll recheck dependencies
EDIT - 24.12.2014
I see that people keep coming to this question I decided to add a little something.
The answer I gave was for the case when you maintain your gems global. Consider using a gem manager such as rbenv or rvm to keep sets of gems scoped to specific projects.
This means that no gems will be installed at a global level and therefore when you remove one from your project's Gemfile and rerun bundle then it, obviously, won't be loaded in your project. Then, you can run bundle clean (with the project dir) and it will remove from the system all those gems that were once installed from your Gemfile (in the same dir) but at this given time are no longer listed there.... long story short - it removes unused gems.
You must use 'gem uninstall gem_name' to uninstall a gem.
Note that if you installed the gem system-wide (ie. sudo bundle install) then you may need to specify the binary directory using the -n option, to ensure binaries belonging to the gem are removed. For example
With newer versions of bundler you can use the clean task:
$ bundle help clean
Usage:
bundle clean
Options:
[--dry-run=only print out changes, do not actually clean gems]
[--force=forces clean even if --path is not set]
[--no-color=Disable colorization in output]
-V, [--verbose=Enable verbose output mode]
Cleans up unused gems in your bundler directory
$ bundle clean --dry-run --force
Would have removed actionmailer (3.1.12)
Would have removed actionmailer (3.2.0.rc2)
Would have removed actionpack (3.1.12)
Would have removed actionpack (3.2.0.rc2)
Would have removed activemodel (3.1.12)
...
edit:
This is not recommended if you're using a global gemset (i.e. - all of your projects keep their gems in the same place).
There're few ways to keep each project's gems separate, though:
I seemed to solve this by manually removing the unicorn gem via bundler ("sudo bundler exec gem uninstall unicorn"), then rebundling ("sudo bundle install").
Not sure why it happened though, although the above fix does seem to work.