I’d like to put in another vote for this feature!
I use Mendeley as a bibliographic manager and pdf annotator, and I absolutely rely on it to organize and rename the files themselves — not just the metadata.
Not only does this keep my files clean, neat, and easy to find, it also (and this is really crucial) keeps me from having to slow down while capturing texts. I don’t have to worry about finding the precise folder, etc. Rather, I can drop the text into Mendeley and know that it will be properly organized — even if I don’t have time until later to come back and add the proper metadata (Mendeley renames the file anytime I make a change to the document title).
I’ve been trying out Trophy and it certainly has some great capabilities, but this feature is so important to me that it’s likely to be a dealbreaker. I’m a bit of a messy researcher, and I need my software to limit, rather than magnify, the mess I make. (Though I realize this might not be as important to other users.)