I was wanting to test some of the capabilities of liquids in the Q3 engine for some map ideas I have, but when I tried using some of the premade liquid shaders in some of the maps (including non-official maps) the brush always ended up solid (they still had wave effect)! I saw the "walk on water" bug mentioned by another noob mapper in the forum, but little help was given other than how to "roll your own" shader. I was finally able to find a water shader to use that worked. It was the one in Karith. And mind you I am using it directly from the Karith pk3. Didn't feel like making my own shader yet so I set this aside for later. Then I started implementing a map idea that calls for lava. I decided to use (at lest temporarily) the lava shader from Thermal, but I ended up with the same problem! At that point I was really going nuts. The shader works fine in Thermal, but spazes out in my maps! What is going on here?!?! Temporarily put the Karith water shader in place of lava and planned to make my own lava later. Finally, this morning sweet inspiration ran me over (will post picture of the tire marks later). The shader scripts look the same in both custom and offical trem maps. Official works, custom don't. The shader effects that affect brush content are evaluated at compile time by q3map2. Must be a compile error! I ran a compile of my map with the Thermal lava shader and checked the build process. Q3map2 can't find thermal.shader, but can find karith.shader! The custom maps are downloaded to my /home/mike/.tremulous/base folder, but q3map2 didn't seem to know about the folder. Instead it was attempting to use /home/mike/.q3a/base!!! I looked into the source for q3map2 and it turns out that the user folder is hard coded into q3map2. The user's game directory name is selected when you set the -game option. My setup of GTKRadiant 1.5 (mostly default based on instructions at the wiki) tries setting "-game tremulous", but there is no "tremulous" option in the q3map2 source so it defaults to quake3. This was no problem when Tremulous was a Q3 mod, but now that it's standalone it needs a game_tremulous.h file to be added to the q3map2 source. Looks easy enough, so I will submit a patch when I have time. For now I have a temporary work around (sorry, Linux/Unix only, though I don't think the problem affects Windows, because I've never seen individual user folders for Q3 based games in Windows

).
Make sure you have a /home/username/.q3a directory. Then symlink /home/username/.tremulous/base --to--> /home/username/.q3a/base
If you don't plan on ever playing Q3 then you have the option of symlinking /home/username/.tremulous --to--> /home/username/.q3a
This is needed to make any shaders work which are stored in /home/username/.tremulous and have compile-time commands.
--crap--
And fellow noobs, remember to add the shader script names to your shaderlist.txt file.
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see below for a clearer explanation