This patch is in human readable form, not in diff format. This has the advantage that it will always work, provided that the user understands the change :-)

Required actions:

(1) Add the files ser_avrdoper.c and ser_avrdoper.h (contained in the attached ZIP archive) to the source directory.

(2) Edit Makefile.am, search for ser_posix.c and add a similar line for
ser_avrdoper.c.

(3) Edit stk500v2.c and search for "usbdevs.h". Immediately after

    #include "usbdevs.h"
add
    #include "ser_avrdoper.h"

Then search for "stk500v2_open" (first occurrence), advance to the line

    pgmtype = PGMTYPE_UNKNOWN;

and after it add the followint code to the function:

    if(strcasecmp(port, "avrdoper") == 0){
#if defined(HAVE_LIBUSB) || defined(WIN32NATIVE)
        serdev = &avrdoper_serdev;
        pgmtype = PGMTYPE_STK500;
#else
        fprintf(stderr, "avrdude was compiled without usb support.\n");
        return -1;
#endif
    }

(4) Re-run autoconf. This is done by running

    ./bootstrap

This step is required in order to propagate the changes in Makefile.am into
Makefile.in. If you can't get autoconf to work, you can attempt the more
complicated edit in Makefile.in instead.

Documentation updates:
One paragraph has been added to avrdude.1 and avrdude.texi. The
paragraph has been marked with dashed lines.

==================
avrdude.1
==================
....
.Pp
As the AVRISP mkII device can only be talked to over USB, the very
same method of specifying the port is required there.
---------------------------------------------------------------
.Pp
For the USB programmer "AVR-Doper" running in HID mode, the port must
be specified as
.Ar avrdoper.
Libusb support is required on Unix but not on Windows. For more
information about AVR-Doper see http://www.obdev.at/avrusb/avrdoper.html.
---------------------------------------------------------------
.Pp
For programmers that attach to a serial port using some kind of
higher level protocol (as opposed to bit-bang style programmers),
.Ar port
....


==================
avrdude.texi
==================
....
As the AVRISP mkII device can only be talked to over USB, the very
same method of specifying the port is required there.

---------------------------------------------------------------
For the USB programmer "AVR-Doper" running in HID mode, the port must
be specified as @var{avrdoper}. Libusb support is required on Unix
but not on Windows. For more information about AVR-Doper see
@url{http://www.obdev.at/avrusb/avrdoper.html}.
---------------------------------------------------------------

For programmers that attach to a serial port using some kind of
higher level protocol (as opposed to bit-bang style programmers),
@var{port} can be specified as @code{net}:@var{host}:@var{port}.
In this case, instead of trying to open a local device, a TCP
network connection to (TCP) @var{port} on @var{host}
is established.
....