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I explicitly go look on my Mac, and then I have to remember what I called the project folder, etc.
Without this, I'm stuck with random Project directories that might hang around long after the project is closed, and then I forget what project it was for, and whether or not I still need it, etc.
I mange my /Users/preston/Projects/ folder as a list of "active" projects.

You should be able to name a project folder the same as the project in OF, it seems that would remove the name ambiguity.

An interesting and simple applescript would:

For any given action, check to see if there was a project folder for the project, and if so - open it, and if not, create it. There would still be no indication visible whether one existed or not...

2. In email, here's my real problem--if I want to capture the task in OF, great, I can do that. But if the task involves replying to the email, or if there are notes in the email related to an attachment, both of which I need to keep, then I need to keep the email somewhere, I can't get rid of it. But I don't feel like I can just have a single folder named "Projects" and just dump all emails into it that I clipped into OF--then when I finish a project I have to remember which emails were related to it and delete or file them into a reference folder.
I actually just keep all my messages in my inbox. If I need to act on them through OF, I capture them into OF. If I need to act on them just in Mail, then I flag them. I then archive my inbox once a year. I've been doing this for quite a few years and find that smartfolders and searching have eliminated any need for additional "filing" of email.