Is there a suggested method to store and version control a project alongside cocos2d-x?
It seems like the best method would be to keep them in separate repos, and re-direct the personal project to use the output of the cocos2d-x build, using relative paths. However, it seems like the template guides you to keep your project in the root of cocos2d-x. I guess another option would be to keep it within cocos2d-x, and make the personal project a sub-module.
Also, when a new version comes out, is it suggested to build a new project shell, and re-populate it with the contents of the existing project? It seems like there is a lot of change happening, which could easily be missed in a port. If so, re-directing the dependencies every major release could get painful. Perhaps a major-version porting guide would quell this concern.