Yes, good point. I suppose when you think of it in that way it would never work as I do need to keep track of my processes, meaning, when I see it then I want to act on it right away, not run a script, go to another file, etc.
This work-flow combined with Freeter (and some professional organization help to put my directories in more logical order) is really helping tremendously. As I had posted elsewhere, I am still learning about the .less file and the hierarchy of what changes text and what does not. I have made a good deal of progress and from that, I am having gaining new confidence in having many projects tracking on a single TaskPaper document, 13 at present count.
When I start work on my book, I will give that it's own TaskPaper document but for the most part I am learning to think of this as a central organization schema. That is to say, I don't have to use it and probably should not be using it as a Folding Text or a compete writing tool such as WriteRoom. What I can do is track my notes, thoughts, tasks and all the rest.
Instead of seeing TaskPaper as a Swiss Army knife of sorts, I am starting to see it - or at least use it, as a tool to locate and track my ideas, my progress, and my processes.