After much searching and reading I'm managed to compile Marine Bot and Waster Bot (both Frank McNeil projects) for Linux. Here is what I've learned. I'll post it here in case anyone else is searching for the answers that I was searching for.
I am using Debian GNU/Linux 3.1 Sarge with gcc 3.4. I guess different Linux distros have different ways of managing packages, so whatever distro you are using will determine how you install this. On Debian it is "apt-get install gcc-3.4" I don't know whether I needed to or not, but I uninstalled gcc 2.95 first - "apt-get --purge remove gcc-2.95".
First get a hold of the patched hlsdk, you can find it
here. [url=http://metamod.sourceforge.net/files/sdk/hlsdk-2.3-p3.tar.gz]hlsdk-2.3-p3.tar.gz[/ur] (this link will obviously be outdated as soon as a new version is released, but hopefully you can just get it from the page link)
1. Untar hlsdk-2.3-p3.tar.gz (move or copy the archive to /usr/src and run this command, "tar -xvzf hlsdk-2.3-p3.tar.gz") into your source directory. On Debian Sarge it is /usr/src. It is worth noting that if you are a nOOb like I am, you may think you can unpack it anywhere and compile it, as I have read in more than one set of instructions. However in Debian Sarge, it appears that you
must do your compiling in the /usr/src directory.
2. Unpack your bot source into your hlsdk multiplayer directory (on Debian it will be /usr/src/hlsdk-2.3-p3/multiplayer). This was where I went wrong in the first place. I didn't realize you needed to have the bot source folder in the hlsdk directory structure.
3. Navigate to your new bot directory (/usr/src/hlsdk-2.3-p3/multiplayer/whateverbot).
4. Run "make" inside your bot directory. Before I run "make" I will also run "make clean", although you will only need to do this if you have run "make" and it has failed.
5. Now I'm afraid that this is where it can get complicated. If everything goes well, your bot will compile and you will have a brand spanking whateverbot.so file in your /usr/src/hlsdk-2.3-p3/multiplayer/whateverbot directory. However, chances are good that it won't compile the first time you try, and you will have to fix something. All I can say at this point is that Google is your friend, and you will have to probably plow through alot of pages before you find the information you need to fix the problem. Pay attention to what file the error occurred in, and look up the line number for clues. I find that using the generic error can help you find answers, there don't seem to be many Half-Life specific bot help pages out there - although I expect the archives for Botman's old forums are a good place to look as well, although I'm afraid I don't know exactly where to find them. Remember if a page won't load from you Google search you can often get the information on that page by clicking on the "cached" link.
6. Obviously once you've compiled your .so file you will need to install it wherever it needs to be installed to run it.
And this is my newbie's guide to compiling Half-Life bots on Linux. I'm thinking of a new slogan, "Newbie Power! By Newbies, For Newbies! Celebrate the nOOb Within!" - closely related to that old chestnut about "the blind leading the blind..."