init.rb

require 'redmine'

Redmine::Plugin.register :my_plugin do
  [...]
    
  project_module :my_module do
    permission :read_my_stuff, :my_controller => [:first_action, :second_action]
  end
end

my_controller.rb

class MyController < ApplicationController
  unloadable
  before_filter :find_project
  before_filter :authorize

  def first_action
    # only entered if user has read_my_stuff permission and the project has the module my_module enabled
    [...]
  end
end