wyBuild supports drag & drop. Also, when you add a folder it add everything inside that folder (including other folders and files).
So... not quite sure what you're asking. wyBuild already supports "recursively" adding folders. In that you add a folder and it adds the folder and everything it contains.
>> "One more question is, if I have 2 products then on the server, a single update folder will do or need separate folders for each product/project?"
Completely up to you. If there's no product name conflict then they can share the same folder.
>> "Also, consider renaming 'File' menu to 'Project'"
Not next version. Maybe eventually.