this pull request sums up support for adding chapters via -add-chapters and -add-chapters-from-cue. The former takes start/end and title of a chapter, while the second reads all chapters in a given cue file.
Please pay extra attention during the review (I'm pretty new to python and some of it might be java-ish).
I started playing with and testing this patch.. a few things I noticed. There is no way to remove chapters with this interface. Also, it seems that each chapter added should have the element ID specified, that way you can change a chapter (not just add) by referring to its element ID. This ID could also be used for --remove-chapter. Thoughts?
unfortunately I won't have time to work on this in the foreseeable future and honestly I only care for '--add-chapter' anyway. I can understand that you only add features if it fully supports add/edit/remove.