When I say that I “use the Finder” to organize project information, I just mean that I use the directory structure. This allows me to access and modify my data with any program, through spotlight, through the terminal, over a network share, etc. This seems to me to be far more flexible than keeping everything in a particular program’s bundle, and it seems very different to me than using an all-in-one task-oriented program.

I appreciate the fact that it might not be Scrivener’s fault that Pages and Word don’t understand RTF footnotes. Nevertheless, I must use one of those programs at some point in my process. It would be great if I could just write in Scrivener and take care of only minor little details in a word processor. Unfortunately, even if footnotes ended up formatted correctly, the text that I end up with out of Scrivener is just flat.

As for some commnets below:

MultiMarkDown: I’ve tried using it to create structured, footnoted documents, with similar problems when exporting. I use TextMate & MarkDown for web writing and note-taking. But not for complex documents that have to end up as printed documents and PDFs.

It’s great if you, as a writer, never have to worry about formatting, so it doesn’t matter to you that RTF footnotes aren’t read correctly, and styles are not used. Unfortunately, at my place on the totem pole, everything is my responsibility.

Ideally, I’d be smart enough to use LaTeX. I did for a while as an English major, after spending weeks getting the templates for MLA styling just right. Unfortunately, there are no templates that are even close to the kinds of documents I need to produce nowadays (that I can find), and I lack the chops to create my own. (And having to manage a separate font system than OS X’s built-in fonts is kind of awkward.)