http://savannah.nongnu.org/projects/avrdude
AVRDUDE with some modifications for custom non-standard baud rates on Linux (as long as the hardware supports it).
Slight issue though - bytes start being dropped if they're not read fast enough, even if they're only being sent in chunks of 128. Stay below 230400 baud. If you really want super fast uploading then you'll have to disable verification (-V).
Custom bauds already work on Windows and has no problems with fast baud rates.
gcc
autoconf (and some other auto stuff which is normally installed along with autoconf)
libtoolize
apt-get install gcc autoconf libtool
libelf
- Support for uploading .elf files
libusb
- Support for programmers that use libUSB like USBasp
libftdi1
- Support for special functions of FTDI chips (not needed if you're only using the serial function)
libhid
- Support for programmers that use some kind of HID thing
apt-get install libelf libusb libftdi1 libhid
NOTE: libftdi1
might be called libftdi
chmod +x ./bootstrap
./bootstrap
./configure
make
Test run
./avrdude