Every major project I work on has documents in a folder.
Using mobile devices has been a productivity booster but storing the documents is a pain. For instance, OmniGraffle for iPad is amazingly useful but it stores documents inside its sandbox and not in my project folder.
My Markdown-formatted notes for the project live in a Dropbox folder. To get to those notes, I use a Dropbox-FOLDER-enabled, markdown-enhanced text editor. That editor is Nebulous Notes. I’d rather use Byword but it is a royal pain in the behind to manually type a different Dropbox folder name into its preferences. So Byword gets used for a current project and Nebulous gets used for everything else. Which is a lot.
I look forward to a project folder solution supported natively is iOS.