Flashing the Commander X16 SMC

Programming the SMC with avrdude would look something like this:

avrdude -CATTinyCore\hardware\avrdude.conf -v -pattiny861 -cstk500v1 -PCOM3 -b19200 -Uflash:w:firmware_with_bootloader.hex:i -Ulfuse:w:0xF1:m -Uhfuse:w:0xD4:m -Uefuse:w:0xFE:m

Above command is borrowed from Wavicle and slightly modified.
For more information about avrdude, have a look at its documentation.

When programming the SMC with a minipro (TL866A or TL866II) and the Xgpro software, it is necessary to specify the fuse bits manually.
The hex file with bootloader can be loaded directly into the software but the fuse bytes needs to be set like this:

Note that the fuse bytes, marked with red, are the same as in the above avrdude command