Arty 7: Is uploading from Freedom Studio using Altera JTAG clone or Usb possible?

I already have a Altera Jtag clone available and buying the offically supported Debugger is getting a bit expensive atm (mostly due to import customs)
I was looking at a couple of alternatives

  1. Altera JTGA: What modifications to the Freedom Studio might be necessary to make it use the altera cable rather than the omlix one?

  2. uploading an entirely new .mcs with my Freedom Studio project binary linked:
    After doing the elf to bin objcopy, is it possible to modify an existing .mcs to include the new code rather than building the whole mcs again from scratch?