The posix filesystem layout doesn't provide an easy way of enumerate all files belonging to a given program. The traditional windows (98?) layout of one app in one folder conversely doesn't easily allow enumerating all binaries. Or all manual entries. Etc
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
