Copying this over from the original here - Aloshi#401
I took it for granted that this was how it worked by default but apparently not.
When using "gamelist-only", ES should not bother scanning for files itself, it should assume that the gamelist is correct (hence telling it just to use the gamelist and not scan). The rom folder and file extension options in the es_systems file shouldn't matter when using this flag as they won't be used.
This would also solve issue Aloshi#370 as it wouldn't matter what the ROM file path was set to, it would just "run" it without checking.
Not 100% sure if this still applies to your new branch, but I didn't see anything addressing it directly when I scanned through.