Please make mods live in their own separate subdirectory with whatever layout inside that your engine requires - so inside each mod directory is the config file, README (please, I know this is an out-there wish but enforcing a README so people provide something giving a URL to find out more info about the mod would be a real win!), a “models” subdirectory with the models, a “scripts” subdirectory with the Lua code, and so on. The game engine scans and collates all those subdirectories, easy-peasy.
This will make mod installation, management, uninstallation and distribution significantly simpler than most games that currently provide modding capability. No problems with collisions between mods either.
If possible, allow mods to exist as .zip files which have an internal layout matching the engine requirements. Then users just have to grab the .zip mod file and place it in their mods directory and go! No mess, no fuss!
Also, a good website with tagging, rating, feedback and community moderation right from the get-go would be a big win.