Make lineage assignment into a model object

[johnlees]

Move the existing code so that it follows the inheritance structure of the other models.
Changing the command line options to give model type when using --fit-model would also make sense.

[nickjcroucher]

Since a75cb4f, the lineage assignment code should be in the correct part of the main routines for conversion to a model type. I've put in some comments where there are temporary fixes to allow this which will probably need to be undone (e.g. where there is a model.save() command).