[michaell2]

don't know of any such tools, so instead I perform the task manually. If I want to better understand how some feature works, I write down in a text file what methods are involved, what method calls which etc. That way at any given time I have to answer fairly simple questions, but the accumulated info in the notes can then be used for more sophisticated reasoning. In other words, analysis :)

[davidfm]

That's exactly what I find myself doing, but: I don't like paper As things change I find myself rewriting the same stuff over and over It feels like it should be easier/more effective if automated

[michaell2]

yep, that's why my comment mentioned using a text file for notes, not paper. I usually edit it using IDE rather than text editor to take advantage of the convenient cut-paste a line of text with CTRL-X / CTRL-V without highlighting by mouse.

Then again, my nestgrid project http://www.nestgrid.org (the desktop version) is IMHO, among other things. the future of this sort of notes taking but I have not yet gotten around to using it "in production".