I'm hopeless at modding, but I'll try to help with the first bit
Agent Smith in Quake Matrix v0.5 is a new model and skin. It's in the Matrix PAK0.pak as smith.mdl. Because the size and animations of it are different from the normal player model, I don't think there is an easy way to "play" as Agent Smith in the StarTrek mod. However, you could easily replace the player model skin, make him look a bit like Agent Smith, and use that in the StarTrek mod. You are going to need some tools...
Pak Explorer
http://www.quaketerminus.com/tools/pakexplr.zip
Pak Explorer allows you to view files within a Quake or Quake 2 .PAK file, extract them, and insert them as well.
Qview123
http://www.quaketerminus.com/tools/qview123.zip
A quick and easy model viewer. Will display Quake1, 2 & 3 model formats.
QME 2.3
http://www.quaketerminus.com/tools/quakeme23.zip
Animation viewer and texture editor for Quake MDL (model) files. You can use the "import texture" feature in this program to very quickly swap skins.
Others
http://www.quaketerminus.com/tools/250Quake1Skins.zip
250 mixed Quake skins
http://www.quaketerminus.com/tools.htm
A few other Quake tools to get you started
Agent Smith test PAK thingy
http://www.quaketerminus.com/temp/smithskin.zip
A test PAK I made to help. If you place this in your Startrek mod directory, you should find you are playing a "Agent Smith type" looking guy... sort of. I made it using bits of other people's skins, and glued them together - i take no credit.
Some instructions.
1. Take the test pak file above, and use the Pak Explorer tool to see what's in it.
2. Extract the player.mdl somewhere (desktop or something)
3. Open the model in Qview123 if you want a quick look at it.
4. Close that program, and open player.mdl in QME 2.3
5. Use the "File" > "import texture" feature to change skins.
6. Save the model, and replace the old textured player.mdl in the Pak file, with the new one.
Okay, that's very quick, but hey I've helped a bit. You need to start messing around with the various programs to get a feel of what is going on. Things will start to fall into place.
P.S. Be careful you don't accidentally replace your Quake/ID1/ PAK0.PAK & PAK1.PAK files.
The Agent Smith model made by the Quake Matrix team.
The test skin I glued together.
