Yes! But if you compile the source code where is it compiled to?
I think AVRDude is the way to upload files to 'duino...
Is that the case?
If so it can't be done at the HEX file level surely.
There's also ways to upload .hex files in a standalone methodhttp://www.gammon.com.au/forum/?id=11638or commercially withhttp://www.kanda.com/products/Kanda/HH0110.htmlwill do the fuses & load program.