Tinderbox has gotten significantly better since it's 2014 iteration. I use it off and on, but it's never quite sunk in for me. There are a few primary reasons. Notes are a pain for me to get formatted in a manner that I like and is consistent. I could do this, but never quite get there because The way I want it set up takes a lot of work and fiddling and ends up being more work that it's worth (for me) and it's not scaleable without a huge amount of work arranging things, or losing items in deep outline hierarchies. Basically, I end up fiddling more than I do working. I've gotten very close to the end of the fiddle factor, and to where it starts to function for me, but then I find something where I can't view it the way I need to and get frustrated. Having said all this, it's prototypes, agents and rules are extremely powerful and would probably do a lot of what you are looking to do based on some of the posts here. The learning curve is steep, but the power it provides you to surface, organize and represent notes is unparalleled.