Ok, so let's say you arrange your folders to acommodate for that. you have /files/$user/$program/$file. That's basically what a primary key in a database looks

Ok, so let's say you arrange your folders to acommodate for that. you have /files/$user/$program/$file. That's basically what a primary key in a database looks like. If you want a secondary index, what databases often do is just create a second table with a different primary key, with the value being primary keys of the main table. We can model that in a filesystem as well, of course. So if I want one filtering by file type and one filtering by month of creation, then I can create /files/$program/$file and then ln -s /files/$program/$file /files/month/$month/$file