Hello,
I believe there is a bug when using the texture packer via export. It seems when exporting, the texture packer doesn't take into account the
combine SubDirectories
or
Flatten Paths
check boxes. However if you use the Texture Packer it does.
I have tested in command line and in editor and achieve the same results.
We are in a, maybe not so unique, unique position where we are using Sprite Lamp and Spine, on a on going project. It is suggested that when using sprite lamp you should make (upto)4 copies of the atlas that gets exported from spine and shade them. However, this doesn't make much sense on a project where things can be added, taken away from or changed constantly. Our solution is to shade all of the images individually then use the texture packer to pack them into the correct files i.e. Lighting Left, Lighting Top.... This works great, but it obviously requires the all the outputs to be the same. This is when I stumbled upon the problem. (if someone is aware of a better way to do this, im open to suggestions)
Because of this bug we have to, essentially, export the project twice. Once via export, and again via texture packer and replace the .atlas and image file(s)