Yes please, it would be very good to keep track of already uploaded files. And when selecting "upload folder/file" only modified files gets uploaded.(besides whatever there is git or not on project )
It would be very good too, if you can save the list of already uploaded files on a session file ( internal if possible, not on project directories. )
Handy probably is to add a "clean uploaded file cache" menuitem, to forget these entries.
This way upload command will work very fast in a very practical manner.