You have already activated X, but your Gemfile requires Y

Using bundle exec is the right way to do this.

Basically what's happening is that you've updated rake to 0.9.2 which now conflicts with the version specified in your Gemfile. Previously the latest version of rake you had matched the version in your Gemfile, so you didn't get any warning when simply using rake.

Yehuda Katz (one of the original Bundler developers) explains it all in this blog post.

To avoid typing bundle exec ... all the time, you could set up an alias or function in your shell for commands you commonly use with Bundler. For example this is what I use for Rake:

$ type bake
bake is a function
bake () 
{ 
    bundle exec rake "$@"
}

Try bundle clean --force

It removes every system gem not in this bundle

If you have a reason to keep the current version of rake (or whatever other gem is causing the problem), matt is correct, the best way to do this is to run bundle exec. This uses the version specified in your Gemfile instead of using the newest version of the gem you have installed. (nathan.f77 has a good solution below if you don't want to type bundle exec every time you run rake)

Otherwise, if there is no reason not to update rake, you can run

bundle update rake

This will actually update your Gemfile.lock to use the newest version of rake instead of having to run bundle exec every time.

Note: if you run just bundle update this will update all the gems in your Gemfile instead of just rake, which probably isn't what you want, because if something breaks in your application you won't know which gem update caused it.

The less recommended way to keep the older version without having to use bundle exec is to uninstall the newer versions of rake.

$ gem uninstall rake

Select gem to uninstall:
 1. rake-0.8.7
 2. rake-0.9.2
 3. All versions
> 2
Successfully uninstalled rake-0.9.2

This works, but if you are working with multiple apps that use different versions of rake, this can be a pain because you will find yourself constantly having to install and uninstall different versions.

Last time that this happened to me, I had updated all my gems. I did a gem uninstall rake and it listed version options. I picked the newer one, and then I did not have to use bundle exec anymore.

Basically, if you use bundle exec it uses whatever gem version is in installed by your bundle, so what is in the Gemfile. Without bundle exec it uses whatever version is your system default.