yeah the 3DS poses a big problem for distributing game mods legally
notable mentions are
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Re-encryption and smart data management can result in very practical xdelta patches....but this method is much more restrictive, you need to keep files sizes exactly the same, if you shrink or enlarge any file compared to the original it throws off the romFS layout, which combined with the encryption which means you won't get a small patch and you will be including a bunch of the original romFS's contents
but for small mods, config editing, stuff like pokemon wild encounter mods translations (with management of filesizes) this is the most effective method and can result in patches of around 5mb which can be applied directly to a encrypted rom
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next up is the good old auto script for extracting the rom, replacing files and rebuilding, this is probably the most versatile, but it does require the end user to generate their own xorpads....but once they do that everything else can be automated, be it patches for games that use large files where you only edited a small section of the original file, or if you created full replacement files a straight swap over of stuff
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NTR plugin + required modded files
this one is really easy, but for example if you only edited 2kb of a 20mb file, NTR would still require the whole replacement file to be included, which brings you back to the more "illegal" side of things....plus layeredFS is 4.x only for o3DS users, and won't play 7.x games unless your on a n3DS.
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and finally the "fake update"/ cia patch method....seeing as atm the only way people have got this working is by basing their work on real patches, and afaik this requires the cia patch to include the games original code.bin file....technically i dont think this would ever be "legal"....unless you go through the same troubles as as the above options (making people decrypt and patch, making your own .xdelta patch...etc, which undermines the usefulness of .cia patches to legally distribute rom mods....but it is more convenient for the end user if the "legal" issue doesn't bother you
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truth be told, no matter what option you go with, someone will probably end up making a full pre-built .3ds/.cia and distributing it at the usual places, so lazy people who cba making it themselves will probably head there to get it pre-built anyway, so i wouldn't worry about making it super easy, just as long as it works