I'd do it manually.
Create a new layer, call it 'Cuts and Folds' and add 0.25pt solid cut lines or dashed fold lines in a spot colour you're not using in the job.
Make sure you set the colour to overprint so it doesn't knock out any detail in your artwork too.
Your print house should be able to pull the information they need out of the file, even if you send them a composite PDF.