Once a large technology is made from sufficiently intertwined parts, there is no way to order an exposition of it such that strongly-connected ideas are always close together.
Spaghetti doesn't want to be free.
The current version of the-software-that-runs-CAREO has suffered pretty severely from this spaghetti syndrome. We're planning the next version, which is a complete rewrite, to be much more modular. Using smaller bits of functionality, hopefully nothing reaches the spaghetti critical mass.
Of course, parallels could be drawn along the lines of Linux (monolithic macrokernel) vs. Darwin (microkernel), but I'm not going to go there at the moment...
UPDATE: I just re-read the excerpted quote, and this quasi-random thought popped into my skull.... Spaghetti wants to be written. Just like the One Ring wants to be found. Only vigilance can prevent it.