Thanks for helping people out here while i've been away
@HeartBound .
@Yudowat and all others asking, FITX isn't an editor.it's a decompiler/compiler. It spits everything out into source code files so you can edit it with any text editor you want instead of being restricted to the features that SM4SHCommand offers. The FITX compiler can also add new commands to empty scripts unlike SM4SHCommand, and you can organize the scripts into any structure you want. The scripts are named correctly only if you specifiy the "-m" option and point it to the correct motion folder. (on 3ds it's data/motion/fighter/[character], and on wiiu it's data/fighter/[character]/motion)
For example, after decompiling you can put all aerials in a folder called "aerials" and all smashes in a folder called "smashes", etc. This system helps immensely for putting the files up on github as source code to take full advantage of collaboration features it offers, along with easily diffing changes since they're are an innumerable number of text differencing applications and websites avaliable.
In the future, SM4SHCommand will no longer support the current workflow of opening a fighter and editing the files raw. Everything will be done in source code, and SM4SHCommand will use FITX as it's backend. Basically, SM4SHCommand will turn into what it should have been from the start and that is an IDE/text editor for fighter creation. wanting to moveset edit shouldn't force people into using any particular application, instead FITX allows people to use whatever they want to do their edits.