I don't know the exact file structure of a .pnd, but I guess it's not much different from the Windows version, in which we have an Images folder containing all sprites, level pieces, etc... as .png images. Really simple to identify and tweak.You'd be able to do that anyway, assuming that the image files aren't encrypted or in some crazy format. You only have to know where the images are in the PND, and what they're named.
No this is not true, it is recommended that you keep a copy inside the PND incase someone else wants to extract it all, the Pandora OS doesn't use the one inside the PND at all, it uses the one appended to the PND archive.The only mandate is that the PXML (the XML identifying all the important stuff about the PND) must be in the root of the PND. PNDs can be opened in 7zip, by the way.
Thanks for the feedback, Jonny DYeah, the new color mechanic sounds good.
Just be sure to differentiate your colored bacteria from Dr. Mario viruses.
I'd like to see the colors correspond to specific abilities of the enemies. E.g. one color has spiky enemies, another has hopping enemies, another has floating enemies, etc. This would also go a little way for the colorblindness issue.
I look forward to seeing how this goes. Here's another small idea: Special colored platforms which only support you if you have the right color collected. Functionally, they could be similar to colored doors, but you could also think of platforming puzzles involving mixed colors and multicolored platforms.