Many of the resources in my project are located in folder references rather than groups, i.e. blue, not yellow folders. This is for a number of reasons - I considered both solutions, and folder references were the better option (I do things like
imagePaths = [[NSBundle mainBundle] pathsForResourcesOfType:@"png" inDirectory:directory];
)
According to this guide I just rename the containting folder, however if I rename any of the folders containing the assets to folder.atlas, this is taken literally as part of the path name, and none of the contents are found.
Is the only way to do this to generate the atlases manually using something like TexturePacker? My code is rather heavily dependent on pathnames, so I would have to do a lot of re-writing...