Ah- so you started out with your project outside of cocos2d, which used the builds stored in the cocos2d project, then essentially moved your project inside of cocos2d-x? I basically did the same thing, because the template changed so much that I found it easier just to make a new project and pull all of my work into it. I was too lazy this time around to change all the dependency paths, though. Maybe some kind of path definition define in the template would make this easier?
Do you version control the entirety of the cocos2d project, along with your project inside of it? I thought about doing that, but if I add more projects later, Id certainly want to version control those independently. This lead me to think about making my project a git sub-module of a cocos2d fork. That seems a bit contrived, though, as cocos2d doesn’t depend on my project, but the other way around.
Unfortunately, I keep coming back to the idea that my personal projects should be outside of cocos2d, which seems like a painful road if there are lots of changes to the cocos2d structure : (