I'd prefer an approach similar to how MAME does it.
Keep assets like Roms, Samples, Screenshots, Manuals, Artworks seperate. Make it up to the user whether or not they want the extras included within their overall emulation library.
As nice as it would be to have an emulator setup where you had the manual, screenshots, box art within easy reach, it has the potential to become massive bloatware where an Atari collection might take 20 Gig instead of 2.
A database file would be preferable IMO - for each game have cataloged the common name for launchable ATR, XEX versions. Allow the user to be able to asssociate other files to a given game (e.g. for self-modified versions).
- MrFish likes this