I want to play this one Quake I mod, but I can't seem to get it to work. Its called "This Alien Earth", and the readme says

It's a bunch of files, and I'm hesitant to put them all into the Quake folder-as that would mean I'd have to pick them out one-by-one when I'm done playing the mod. I play Quake I with NQuake: a source port for Quake. here is the DL link to the mod I'm talking about-> quakeone.com/files...45-alien-earth/

I want to play it, but I don't know how to make a mod directory without replacing anything. The readme says to contact the author, but the readme dates back to 2001...I doubt he hasn't moved on to other things beyond Q1 by now. Can anybody help?

My guess is you downloaded the "taedemo.zip" file. To be honest, that is one messed up Quake mod. The author does not really know what they are doing and have files everywhere. There should be only 2-4 files. A game pak, a readme, a batch file (for windows) and maybe a shell script (for linux).

Personally, I would make a copy of your Quake directory, then extract just the "taedemo" directory and see if that works. You would start the game from the command line with:

<quake engine.exe> -game taedemo

If that does not work, extract the other files, but that will make a mess of your Quake directory too (which is why I said to make a copy :])

This Alien Earth used a bunch of early QSG extensions IIRC (for brush transparency like glass). You'd have to use something compliant for that, like Darkplaces.