I have been having a problem with using Bundler and being able to access my gems without having to require them somewhere, as config.gem used to do that for me (as far as I know). In my Rails 3 app, I defined my Gemfile like so:

clear_sources
source "http://gemcutter.org"
source "http://gems.github.com"
bundle_path "vendor/bundler_gems"

## Bundle edge rails:
git "git://github.com/rails/arel.git"
git "git://github.com/rails/rack.git"
gem "rails", :git => "git://github.com/rails/rails.git"

## Bundle
gem "mongo_mapper", :git => "git://github.com/jnunemaker/mongomapper.git"
gem "bluecloth", ">= 2.0.0"

Then I run gem bundle, it bundles it all up like expected. Inside the environment.rb file that is included within boot.rb it looks like this:

# DO NOT MODIFY THIS FILE
module Bundler
 file = File.expand_path(__FILE__)
 dir = File.dirname(file)

  ENV["PATH"]     = "#{dir}/../../../../bin:#{ENV["PATH"]}"
  ENV["RUBYOPT"]  = "-r#{file} #{ENV["RUBYOPT"]}"

  $LOAD_PATH.unshift File.expand_path("#{dir}/gems/builder-2.1.2/bin")
  $LOAD_PATH.unshift File.expand_path("#{dir}/gems/builder-2.1.2/lib")
  $LOAD_PATH.unshift File.expand_path("#{dir}/gems/text-hyphen-1.0.0/bin")
  $LOAD_PATH.unshift File.expand_path("#{dir}/gems/text-hyphen-1.0.0/lib")
  $LOAD_PATH.unshift File.expand_path("#{dir}/gems/i18n-0.3.3/bin")
  $LOAD_PATH.unshift File.expand_path("#{dir}/gems/i18n-0.3.3/lib")
  $LOAD_PATH.unshift File.expand_path("#{dir}/dirs/arel/bin")
  $LOAD_PATH.unshift File.expand_path("#{dir}/dirs/arel/lib")
  $LOAD_PATH.unshift File.expand_path("#{dir}/dirs/rails/activemodel/bin")
  $LOAD_PATH.unshift File.expand_path("#{dir}/dirs/rails/activemodel/lib")
  $LOAD_PATH.unshift File.expand_path("#{dir}/gems/jnunemaker-validatable-1.8.1/bin")
  $LOAD_PATH.unshift File.expand_path("#{dir}/gems/jnunemaker-validatable-1.8.1/lib")
  $LOAD_PATH.unshift File.expand_path("#{dir}/gems/abstract-1.0.0/bin")
  $LOAD_PATH.unshift File.expand_path("#{dir}/gems/abstract-1.0.0/lib")
  $LOAD_PATH.unshift File.expand_path("#{dir}/gems/erubis-2.6.5/bin")
  $LOAD_PATH.unshift File.expand_path("#{dir}/gems/erubis-2.6.5/lib")
  $LOAD_PATH.unshift File.expand_path("#{dir}/gems/mime-types-1.16/bin")
  $LOAD_PATH.unshift File.expand_path("#{dir}/gems/mime-types-1.16/lib")
  $LOAD_PATH.unshift File.expand_path("#{dir}/gems/mail-2.1.2/bin")
  $LOAD_PATH.unshift File.expand_path("#{dir}/gems/mail-2.1.2/lib")
  $LOAD_PATH.unshift File.expand_path("#{dir}/gems/rake-0.8.7/bin")
  $LOAD_PATH.unshift File.expand_path("#{dir}/gems/rake-0.8.7/lib")
  $LOAD_PATH.unshift File.expand_path("#{dir}/dirs/rails/railties/bin")
  $LOAD_PATH.unshift File.expand_path("#{dir}/dirs/rails/railties/lib")
  $LOAD_PATH.unshift File.expand_path("#{dir}/gems/memcache-client-1.7.7/bin")
  $LOAD_PATH.unshift File.expand_path("#{dir}/gems/memcache-client-1.7.7/lib")
  $LOAD_PATH.unshift File.expand_path("#{dir}/dirs/rack/bin")
  $LOAD_PATH.unshift File.expand_path("#{dir}/dirs/rack/lib")
  $LOAD_PATH.unshift File.expand_path("#{dir}/gems/rack-test-0.5.3/bin")
  $LOAD_PATH.unshift File.expand_path("#{dir}/gems/rack-test-0.5.3/lib")
  $LOAD_PATH.unshift File.expand_path("#{dir}/gems/rack-mount-0.4.5/bin")
  $LOAD_PATH.unshift File.expand_path("#{dir}/gems/rack-mount-0.4.5/lib")
  $LOAD_PATH.unshift File.expand_path("#{dir}/dirs/rails/actionpack/bin")
  $LOAD_PATH.unshift File.expand_path("#{dir}/dirs/rails/actionpack/lib")
  $LOAD_PATH.unshift File.expand_path("#{dir}/gems/bluecloth-2.0.7/bin")
  $LOAD_PATH.unshift File.expand_path("#{dir}/gems/bluecloth-2.0.7/lib")
  $LOAD_PATH.unshift File.expand_path("#{dir}/gems/bluecloth-2.0.7/ext")
  $LOAD_PATH.unshift File.expand_path("#{dir}/dirs/rails/activerecord/bin")
  $LOAD_PATH.unshift File.expand_path("#{dir}/dirs/rails/activerecord/lib")
  $LOAD_PATH.unshift File.expand_path("#{dir}/gems/text-format-1.0.0/bin")
  $LOAD_PATH.unshift File.expand_path("#{dir}/gems/text-format-1.0.0/lib")
  $LOAD_PATH.unshift File.expand_path("#{dir}/dirs/rails/actionmailer/bin")
  $LOAD_PATH.unshift File.expand_path("#{dir}/dirs/rails/actionmailer/lib")
  $LOAD_PATH.unshift File.expand_path("#{dir}/gems/tzinfo-0.3.16/bin")
  $LOAD_PATH.unshift File.expand_path("#{dir}/gems/tzinfo-0.3.16/lib")
  $LOAD_PATH.unshift File.expand_path("#{dir}/dirs/rails/activesupport/bin")
  $LOAD_PATH.unshift File.expand_path("#{dir}/dirs/rails/activesupport/lib")
  $LOAD_PATH.unshift File.expand_path("#{dir}/dirs/rails/activeresource/bin")
  $LOAD_PATH.unshift File.expand_path("#{dir}/dirs/rails/activeresource/lib")
  $LOAD_PATH.unshift File.expand_path("#{dir}/dirs/rails/bin")
  $LOAD_PATH.unshift File.expand_path("#{dir}/dirs/rails/lib")
  $LOAD_PATH.unshift File.expand_path("#{dir}/gems/mongo-0.18.2/bin")
  $LOAD_PATH.unshift File.expand_path("#{dir}/gems/mongo-0.18.2/lib")
  $LOAD_PATH.unshift File.expand_path("#{dir}/dirs/mongomapper/bin")
  $LOAD_PATH.unshift File.expand_path("#{dir}/dirs/mongomapper/lib")

  @gemfile = "#{dir}/../../../../Gemfile"

  require "rubygems" unless respond_to?(:gem) # 1.9 already has RubyGems loaded

  @bundled_specs = {}
  @bundled_specs["builder"] = eval(File.read("#{dir}/specifications/builder-2.1.2.gemspec"))
  @bundled_specs["builder"].loaded_from = "#{dir}/specifications/builder-2.1.2.gemspec"
  @bundled_specs["text-hyphen"] = eval(File.read("#{dir}/specifications/text-hyphen-1.0.0.gemspec"))
  @bundled_specs["text-hyphen"].loaded_from = "#{dir}/specifications/text-hyphen-1.0.0.gemspec"
  @bundled_specs["i18n"] = eval(File.read("#{dir}/specifications/i18n-0.3.3.gemspec"))
  @bundled_specs["i18n"].loaded_from = "#{dir}/specifications/i18n-0.3.3.gemspec"
  @bundled_specs["arel"] = eval(File.read("#{dir}/specifications/arel-0.2.pre.gemspec"))
  @bundled_specs["arel"].loaded_from = "#{dir}/specifications/arel-0.2.pre.gemspec"
  @bundled_specs["activemodel"] = eval(File.read("#{dir}/specifications/activemodel-3.0.pre.gemspec"))
  @bundled_specs["activemodel"].loaded_from = "#{dir}/specifications/activemodel-3.0.pre.gemspec"
  @bundled_specs["jnunemaker-validatable"] = eval(File.read("#{dir}/specifications/jnunemaker-validatable-1.8.1.gemspec"))
  @bundled_specs["jnunemaker-validatable"].loaded_from = "#{dir}/specifications/jnunemaker-validatable-1.8.1.gemspec"
  @bundled_specs["abstract"] = eval(File.read("#{dir}/specifications/abstract-1.0.0.gemspec"))
  @bundled_specs["abstract"].loaded_from = "#{dir}/specifications/abstract-1.0.0.gemspec"
  @bundled_specs["erubis"] = eval(File.read("#{dir}/specifications/erubis-2.6.5.gemspec"))
  @bundled_specs["erubis"].loaded_from = "#{dir}/specifications/erubis-2.6.5.gemspec"
  @bundled_specs["mime-types"] = eval(File.read("#{dir}/specifications/mime-types-1.16.gemspec"))
  @bundled_specs["mime-types"].loaded_from = "#{dir}/specifications/mime-types-1.16.gemspec"
  @bundled_specs["mail"] = eval(File.read("#{dir}/specifications/mail-2.1.2.gemspec"))
  @bundled_specs["mail"].loaded_from = "#{dir}/specifications/mail-2.1.2.gemspec"
  @bundled_specs["rake"] = eval(File.read("#{dir}/specifications/rake-0.8.7.gemspec"))
  @bundled_specs["rake"].loaded_from = "#{dir}/specifications/rake-0.8.7.gemspec"
  @bundled_specs["railties"] = eval(File.read("#{dir}/specifications/railties-3.0.pre.gemspec"))
  @bundled_specs["railties"].loaded_from = "#{dir}/specifications/railties-3.0.pre.gemspec"
  @bundled_specs["memcache-client"] = eval(File.read("#{dir}/specifications/memcache-client-1.7.7.gemspec"))
  @bundled_specs["memcache-client"].loaded_from = "#{dir}/specifications/memcache-client-1.7.7.gemspec"
  @bundled_specs["rack"] = eval(File.read("#{dir}/specifications/rack-1.1.0.gemspec"))
  @bundled_specs["rack"].loaded_from = "#{dir}/specifications/rack-1.1.0.gemspec"
  @bundled_specs["rack-test"] = eval(File.read("#{dir}/specifications/rack-test-0.5.3.gemspec"))
  @bundled_specs["rack-test"].loaded_from = "#{dir}/specifications/rack-test-0.5.3.gemspec"
  @bundled_specs["rack-mount"] = eval(File.read("#{dir}/specifications/rack-mount-0.4.5.gemspec"))
  @bundled_specs["rack-mount"].loaded_from = "#{dir}/specifications/rack-mount-0.4.5.gemspec"
  @bundled_specs["actionpack"] = eval(File.read("#{dir}/specifications/actionpack-3.0.pre.gemspec"))
  @bundled_specs["actionpack"].loaded_from = "#{dir}/specifications/actionpack-3.0.pre.gemspec"
  @bundled_specs["bluecloth"] = eval(File.read("#{dir}/specifications/bluecloth-2.0.7.gemspec"))
  @bundled_specs["bluecloth"].loaded_from = "#{dir}/specifications/bluecloth-2.0.7.gemspec"
  @bundled_specs["activerecord"] = eval(File.read("#{dir}/specifications/activerecord-3.0.pre.gemspec"))
  @bundled_specs["activerecord"].loaded_from = "#{dir}/specifications/activerecord-3.0.pre.gemspec"
  @bundled_specs["text-format"] = eval(File.read("#{dir}/specifications/text-format-1.0.0.gemspec"))
  @bundled_specs["text-format"].loaded_from = "#{dir}/specifications/text-format-1.0.0.gemspec"
  @bundled_specs["actionmailer"] = eval(File.read("#{dir}/specifications/actionmailer-3.0.pre.gemspec"))
  @bundled_specs["actionmailer"].loaded_from = "#{dir}/specifications/actionmailer-3.0.pre.gemspec"
  @bundled_specs["tzinfo"] = eval(File.read("#{dir}/specifications/tzinfo-0.3.16.gemspec"))
  @bundled_specs["tzinfo"].loaded_from = "#{dir}/specifications/tzinfo-0.3.16.gemspec"
  @bundled_specs["activesupport"] = eval(File.read("#{dir}/specifications/activesupport-3.0.pre.gemspec"))
  @bundled_specs["activesupport"].loaded_from = "#{dir}/specifications/activesupport-3.0.pre.gemspec"
  @bundled_specs["activeresource"] = eval(File.read("#{dir}/specifications/activeresource-3.0.pre.gemspec"))
  @bundled_specs["activeresource"].loaded_from = "#{dir}/specifications/activeresource-3.0.pre.gemspec"
  @bundled_specs["rails"] = eval(File.read("#{dir}/specifications/rails-3.0.pre.gemspec"))
  @bundled_specs["rails"].loaded_from = "#{dir}/specifications/rails-3.0.pre.gemspec"
  @bundled_specs["mongo"] = eval(File.read("#{dir}/specifications/mongo-0.18.2.gemspec"))
  @bundled_specs["mongo"].loaded_from = "#{dir}/specifications/mongo-0.18.2.gemspec"
  @bundled_specs["mongo_mapper"] = eval(File.read("#{dir}/specifications/mongo_mapper-0.6.10.gemspec"))
  @bundled_specs["mongo_mapper"].loaded_from = "#{dir}/specifications/mongo_mapper-0.6.10.gemspec"

  def self.add_specs_to_loaded_specs
    Gem.loaded_specs.merge! @bundled_specs
  end

  def self.add_specs_to_index
    @bundled_specs.each do |name, spec|
      Gem.source_index.add_spec spec
    end
  end

  add_specs_to_loaded_specs
  add_specs_to_index

  def self.require_env(env = nil)
    context = Class.new do
      def initialize(env) @env = env && env.to_s ; end
      def method_missing(*) ; yield if block_given? ; end
      def only(*env)
        old, @only = @only, _combine_only(env.flatten)
        yield
        @only = old
      end
      def except(*env)
        old, @except = @except, _combine_except(env.flatten)
        yield
        @except = old
      end
      def gem(name, *args)
        opt = args.last.is_a?(Hash) ? args.pop : {}
        only = _combine_only(opt[:only] || opt["only"])
        except = _combine_except(opt[:except] || opt["except"])
        files = opt[:require_as] || opt["require_as"] || name
        files = [files] unless files.respond_to?(:each)

        return unless !only || only.any? {|e| e == @env }
        return if except && except.any? {|e| e == @env }

        if files = opt[:require_as] || opt["require_as"]
          files = Array(files)
          files.each { |f| require f }
        else
          begin
            require name
          rescue LoadError
            # Do nothing
          end
        end
        yield if block_given?
        true
      end
      private
      def _combine_only(only)
        return @only unless only
        only = [only].flatten.compact.uniq.map { |o| o.to_s }
        only &= @only if @only
        only
      end
      def _combine_except(except)
        return @except unless except
        except = [except].flatten.compact.uniq.map { |o| o.to_s }
        except |= @except if @except
        except
      end
    end
    context.new(env && env.to_s).instance_eval(File.read(@gemfile), @gemfile, 1)
  end
end

module Gem
  @loaded_stacks = Hash.new { |h,k| h[k] = [] }

  def source_index.refresh!
    super
    Bundler.add_specs_to_index
  end
end

But when I try to access any of my gems, e.g. MongoMapper, Paperclip, Haml, etc. I get:

NameError: uninitialized constant MongoMapper

The same goes for any other gem. Does Bundler not include gems like the old Rails 2.0 did? Or is something messed up with my system?

Any help would be appreciated, thank you!