This program is designed to store all your arcade data in its own db folder. When you add an instance, it produces an MD5 hash of the file and stores it in the db folder. Only new and unique files are added, but the record of the file and its location in the original folder is also stored in the instance .json file.

You can then create hard links to your desired destination(s).

It is highly recommended to only add the data folder of a game as an instance. Also remember that hard links only work on the same partition, additionally editing/modifying hard-linked files will change the originals in the db so take extra care. Delete a hard-linked file first if you want to replace/modify it!