3dstool VS 3DS-rom-tools

For open-source tools, Project CTR includes ctrtool to extract many 3DS formats including CIA, and makerom to build an NCCH, CIA, or CCI file. It's a bit old so I'm not positive it'll work exactly, but there's a guide on extracting a CIA using ctrtool and 3dstool, then rebuilding it using makerom and 3dstool.

You can rip the game to a cia file using GM9, and then on a PC use ctrtool and 3dstool to extract cia contents, extract the romfs from that, and then extract the romfs contents which will have all the game data files. I will warn you though that everything is in special Nintendo formats and it's different in some games. You may or may not be able to convert them to a normal PC audio format with various tools.

This is the one I have been using (https://github.com/ihaveamac/3DS-rom-tools/wiki/SeedDB-list). Make sure to put it in the same folder as the decryptor.

I use the custom-install program to install games, where you need to provide your own seeddb, so I downloaded one from custom-install's maker - https://github.com/ihaveamac/3DS-rom-tools/wiki/SeedDB-list

For open-source tools, Project CTR includes ctrtool to extract many 3DS formats including CIA, and makerom to build an NCCH, CIA, or CCI file. It's a bit old so I'm not positive it'll work exactly, but there's a guide on extracting a CIA using ctrtool and 3dstool, then rebuilding it using makerom and 3dstool.

Basically, you would need a tool to unpack an FE15 3ds file, load the files into Paragon, edit the skill on everyone you want and then repack the edited files with the rest of the unedited files from the game, and play. If you're wondering how to unpack and repack 3ds files you may find this resource on github to be useful.