I know i may be ennoying but could it be possible to export the different stances in different single files? I have a lot of difficulty cutting and resizing it for Intersect Engine (like 4x4 chara tiles). Thank you for your work!
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My first thought is "that's not meant to be done by this app".
Personally I would use a tool suited for that task (at the top of my head is ImageMagick).
Also, I would prefer to have the animations in a single spritesheet, in order to reduce the graphics card state changes, however, I'm not familiar with the Intersect Engine, so I don't know of that's an option.
That said, if none if these options work for you, I'll probably fit this change in the next release, no problem (the hide body is already done).
ImageMagick might not be the solution for your problem, or maybe I didn't understand it yet.
That said, version 0.4 made this possible (and I completely forgot to mention it).
In the chargen.ini file, the parameter "export_individual_sheets" does this. Set it to true, and see if that solves your problem.