If you have a bunch of mods on your server and get tired of moving files around and worrying about collisions within the mods themselves, you can do this:
1. Create a directory under main to hold each mod (ie. mainckr to hold the CKR mod). If there are mods you like to run at the same time, put them in the same directory.
2. Copy the dll files from your main directory into each of the mod directories you created. There are three of them (cgamex86.dll, gamex86.dll and ffx86.dll). Make sure you only COPY them. You do not want to MOVE them.
3. To activate the mods in any directory, add "+set fs_game main/dir" to your server's command line, where dir is the mod's directory. For example, to activate the CKR mod, you would have "+set fs_game main/ckr" in your command line (without the quotes).
Now, instead of switching files around a lot, all you have to do is edit the directory in your startup.
Please note:
1. The server config file in your command line will determine your map rotation, etc. The mods you run should not affect it.
2. You need to use the forward slash (/) when you identify the directory (ie. main/ckr). Using the back slash will probably still work, but it will generate an error message in the console.
3. I don't think you can set multiple fs_game switches in your command line, so just put the mods you like to run together in the same directory. You do not need to rename them to pak0.pk3, pak1.pk3, etc. (in some other Q3 games you do, but not in MoHAA).
4. If you like to run the same mod in multiple combinations with other mods, just copy the pk3 file for that mod in multiple directories.
Hope someone finds this useful.
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"If your philosophy does not produce corn, I don't want to hear about it." - Red Bear