Extending

It should be safe to edit the generated files because the rails generate script will warn of conflicts on subsequent runs, and allow you to perform a diff for resolving the conflict. However, for deployment scripts, there is a lot you can do by tying into the existing process flow by using the capistrano before/after mechanism. For example,

after "rubber:install_packages", "custom_install" 
before "rubber:install_packages", "custom_install_web" 

# run for all roles
task :custom_install do
  sudo_script <<-SCRIPT
    run_cmd
    other_cmd
    ! cmd_that_can_have_non-zero_exit
  SCRIPT
end

# only run for web roles
task :custom_install_web, :roles => :web do
  put(File.read("local/file"), "/some/file")
end

If anyone has any configuration templates similar to what is provided in generators/vulcanize/templates, please contribute them to the project, e.g. a module for using apache instead of nginx, or postgres instead of mysql, etc.