This thread in the DevonThink forums talks about various uses of DTP, but focusing on the “how to organize your Devon Think library.” There are multiple ways, each having its benefits — after all YOU need to be working with it, so in a way the structure might resemble the way you think or work. But it all comes down to utilizing the powers of teh DevonThink AI: group stuff together that needs to be grouped. Group similar stuff. File Things wherever they might belong. This way the AI learns and will help you later when filing new stuff where it might belong to.
You could also tag your files (e.g. via their comments) and then grab the tagged files via a smart folder (see 43Folders for a detailed article on this). btw a very useful feature that can also be used in Finder.app: You can very easily set finder/spotlight comments via a Quicksilver-Plugin and then assemble all related items with a smart folder (or saved search from spotlight). e.g. Ⅰ have a projects.smartfolder that contains all my current projects’ folders (tagged with “@project,” of course), no matter where they are. You could also be more specific and just get all files tagged with “@recipe” and “@baking”… you get the idea.
Mehr…
Giles Turnbull talks about Tiger’s Spotlight and how it drastically changes the way people work with files.
when Ⅰ heard Brian talking to another journalist:
„The first thing you start doing is cease using hierarchy as a means of storing stuff. Ⅰ know this, because I’ve been using this for a few months and Ⅰ don’t bother to file things anymore. Ⅰ don’t give a rat’s ass where my files are, because Spotlight finds everything for me.“
That’s the crucial, boiled-to-the-bone reality of something like Spotlight. If it really is capable of finding what you need, why bother keeping your stuff in any kind of order?
Ⅰ have had a similar experience when Ⅰ switched to DevonThink for File archival, especially for saving all those snippets and publications Ⅰ come across in daily work and surfing. If Spotlight can keep my other files in order – Ⅰ want Tiger ASAP. Now and if that is the end to the crappy Finder, so be it.
Just wondering: what will DevonThink be like after version 2.0 – when they switch to a file based database – as well as interact with Spotlight? Ⅰ believe this will be even better than just Tiger – but Ⅰ want it now as well 
This screenshot at Flickr shows a good setup for using GTD with DevonThink.
An interesting discussion about the application of DevonThink to GTD can be found here, although there are quite a bunch of questions left unanswered as of the time of this post (2005–03–08 17 : 01 CET)
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