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Folders are an organizing tool outside of the ability to complete the stuff within it. DA might refer to these as "areas of responsibility" (work/finances/etc) or "visions" (30-, 40- and 50-thousand foot views, e.g.).

A "project", in GTD terms, is "a desired result with more than one step to completion". "Call Bob re:painter" is a single action, unless you first need to find Bob's phone number, in which case it might become a project that includes "Search email for Bob's number".

NickM, are all your projects "active", i.e. they're all things you're actively working toward completing? Or do they include things you've put on hold, or are pending, or even already completed?

Also, how many projects are we talking about? (The number seems to have been lost in your post.) I have somewhere around 70 active projects, and the hardest part is finding a project in the list, as once the project is entered, I spend very little time in the project pane.

What has been frustrating you?