Scott M
Ok, I may have a possible solution for you. I’ve recently set this up
to maintain my GTD system. (So take that into account.) However,
since you said you once used text files it should be pretty easy.

I use BBEdit for all of my notes, thoughts, projects, check lists,
someday maybe, etc. (I use it for other things as well but this isn’t
BBEdit-Talk) I keep them in a folder named _GTD that’s easily searchable
with Spotlight. Here’s what it looks like :
(And, yes - it is a nested folder)

Obviously you can choose whatever symbols or non symbols you want.
Where I think this will be more relevant to your workflow is in using smart
folders. I create a smart folder for all related text, graphics, images,
pdf (including Yojimbo) files, etc. I'll add any relevant keywords,
tags, notes in the finder information box and have spotlight search
there. (You can handle the smart folder any way you want this is just
how I like to do it.) This is a nice way to have everything you need for
whatever you are currently working on. When I’m done with the project
and don’t plan on re opening it for at least a few months, I create an .zip
archive of all the related files (For Yojimbo files I’ll export the PDF)
and just delete the smart folder. Done.

What I like most about this system is that it doesn’t rely on any one
application to heavily and keeps things pretty simple. I store the _GTD
folder on a thumb drive but an iPod is certainly just as good. When I head
out any relevant @ Next Actions are printed out (yes - paper), folded
and kept together with a medium size Moleskines reporter notebook.

Just an idea. Hope it helps Scott : )
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