If your roms are already on a Linux/unix/mac, you can use these scrips: https://gist.github.com/ReallyVasiliy/32c33be595408d353e37999ce305ea4d
You need to save each file on the target system, and give them execute permissions (in the terminal, run “chmod a+x move”).
move: moves the roms specified in the file <arg1>, which are contained in directory <arg2>, to a new directory <arg2>/<arg1>. An example terminal command could be:
$ move somewhere/Clones.txt /userdata/roms/fbneo
Will move files specified in Clones.txt from /userdata/roms/fbneo to /userdata/roms/fbneo/Clones
The remove script has the same arguments but simply deletes them permanently instead of moving.