Problem description:

When connecting to pure servers, you need all the .PK3s. But perhaps you don't want them polluting your local copy. For example, mod X has several versions:

z-modx-153.pk3
z-modx-154.pk3
z-modx-155.pk3

Every PK3 includes all the previous files, so it's best to only have the last one (faster loading, and if you run a pure server the clients will only need the last one).

But there are servers still running 153 and 154, so you need them to connect (and some have all three, because the admin didn't delete the previous two).

Right now, your only option is to manage them manually.

Then there's outright pullution. Perhaps there's a server with:

zzzzUberQ3DM6.PK3
zzzzUberSounds.PK3

Once you connect, the .PK3s are autodownloaded. After that, if you start a game (create a server), you get the UberSounds and the modified version of Q3DM6 whether you want them or not (and force them upon other clients if pure). You can delete manually the PK3s, but that's clumsy and you'd need them again to play on that server.

Proposal:

Have an auxiliary storage for autodownloaded / unwanted .PK3s.
For example additionalPK3s\.

Normally, the .PK3s there are never referenced. Only when connecting to a pure server that needs them, they are loaded. Autodownloaded files would go there too. After disconnecting, they would be dereferenced leaving a clean system again.

So you could drop older versions of maps/mods there (to be able to connect to unupdated servers), and if you need a .pk3 which you normally wouldn't use you can put it there too.