I wouldn't say they are useless and incomplete because alot of them are a WIP and I'm sure it's very time consuming and difficult work to actually complete them. I do appreciate what has already been done and the work currently being done.
I had some problems with things launching and such when I first started out using MESSUI or command line, but managed to solve it by putting all the BIOS files in roms directory and all the extra software directories or software lists sub directories (not sure what to exactly call it) also in roms directory.
You can change windows list view to group by type so it looks organized. Then just for kicks I put the exact path to all the systems extra_software in MESSUI.ini
In other words, I have everything in roms directory and haven't had to create a software directory. When I had the BIOS files in a directory named BIOS and the other directories in a directory named software is when I had major problems with command line and or MESSUI with certain things failing launch.
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