OpsWorks, at the moment, does not support a single cookbook directory style. It works to build the repository like this:
delayed_job
recipes
deploy.rb
undeploy.rb
s3cmd
attributes
default.rb
recipes
setup.rb
configure.rb
templates
default
s3cfg.erb
whenever
recipes
deploy.rb
undeploy.rb
Then under stack settings, under custom cookbooks, one can add e.g. whenever::deploy under deploy. For default.rb recipes, once can just add e.g. sphinx instead of sphinx::default.
And after changing and pushing to the repositiory, one has to run the update_custom_cookbooks
command from the deployments page.