What's the solution here? After a few years you end up with huge boxes full of notes, some of which have been appended over and over? Mind maps rarely scale when done with software, paper note-taking just makes it all the more hopeless.
And really, why be so obsessive about conserving every little thought like your stream of consciousness holds some big revelation at the end? That's not how it works. Forgetting and scrapping things is an important part of organizing the mind and the output it produces. On a meta level, this book illustrates very well what happens if that doesn't work.
If we're building a system with the goal of swapping out thoughts and memories, it really has to augment the brain in some fashion. Refining relations between concepts is something the brain is already good at, it would make more sense to help it along in areas where the brain sucks: keeping lists and details. Seriously, open an Evernote account or something and don't worry too much about organization and preservation.
I'm really sorry if this sounds mean, it's not supposed to.
I clicked expecting a well thought out strategy for organizing concept maps on a large scale but instead this is some individuals idea on how best to organize their own thoughts. In fact, not once in the entire document is the term "concept map" even used which makes me think that this person has spent zero time researching established techniques on the subject.
Concept maps are great. I've used them in the past and wish I could get in the habit of maintaining them more often. If you're interested in capturing and organizing your own thoughts, I'd highly recommend you look into concept maps. This on the other hand, I'm not sure what this is and I certainly wouldn't recommend you follow it.
 PS this was not a comment on the validity of the ideas presented, just a comment on the general craziness of individual bloggers.
Madmen do tend to emphasize random words: http://zippythepinhead.com/Merchant2/merchant.mv?Screen=PROD...
(M-x yow, how I miss you.)
"keeping a map of all your thoughts has a freezing effect on the mind."
"you will be IMMOBILIZED for the duration of your commitment"
Sounds like he went mad in the attempt.
I can't help but come to the conclusion he's nuts.