There should be a way to decouple the input and output filenames (database vs. local filesystem source/destination) for mongofiles "get" and "put" commands.

I'd suggest "i filename" for PUT, and "-o filename" for GET, where filename is the source/destination filename (including path), and "" represents reading from STDIN or writing to STDOUT, respectively. Keep "--file" (or maybe "-f" for short) to refer to the filename stored in the database.