Toolchain questions

[rbean]

(The forum software won't let me post actual links, so I'll have to describe where they are

Starting with the main mpguino wiki page, there's a link to some code called mpguino.pde

However, the header of that file says:
//current development moved outside of arduino proper, reference
Followed by a link to something called mpguino.cpp

So, is that second link the most recent code?
Is there some reason the wiki doesn't link directly to it?

Also, if you're not using the Arduino IDE, what is the current toolchain?
(I'd prefer to work under Linux, but I also have access to WinXP.)

Also on the wiki page is a link called 'Theory of operation' at combustory.com
But that link isn't responding. Is that still a good link, and if not, does anyone have a mirror of it? Or other sources that would help a newcomer understand the code?

Also, is there some way to selectively compile in certain features and not others, to save space? I'm thinking of experimenting with various new features, but it will be a while until I can get around to it. Just trying to understand the code for now.