Ok - I've resolved this. Apparently, the git repo doesn't require the config.xml and index.html to be in the root, that's only a requirement of the zip upload.
So my repo is just:
And build seems to work with this configuration (as does phonegap running locally).
There seems to be a lot of confusion about this. Surely the zip requires a www folder with index.html and config.xml ... mine has that ... I think some clear clarification is required as to the project folder structure that is required and whether that changes (hopefully not!) between various methods.
One is surely zipping MyProject folder which has a www inside it ... otherwise why have a www folder at all.
MyProject <=== zip this