Im loosing my head here.

C:\MyStuff\Work\Thesis\arduino-1.0-windows(2)\arduino-1.0\hardware\tools\avr\bin

avrdude.exe in that directory.

Now I go to command prompt. To that directory. try avrdude -h... all the commands pop up.
But then when I copy paste your line it says it cant find config file.

I saw theres a config fille in this directory
C:\MyStuff\Work\Thesis\arduino-1.0-windows(2)\arduino-1.0\hardware\tools\avr\etc\avrdude.conf

How do i link the exe to it? /should I just go change settings manually.

C:\MyStuff\Work\Thesis\arduino-1.0-windows(2)\arduino-1.0\hardware\tools\avr\bin

#------------------------------------------------------------

ATmega328P

#------------------------------------------------------------

part
id = "m328p";
desc = "ATMEGA328P";
has_debugwire = yes;
flash_instr = 0xB6, 0x01, 0x11;
eeprom_instr = 0xBD, 0xF2, 0xBD, 0xE1, 0xBB, 0xCF, 0xB4, 0x00,
0xBE, 0x01, 0xB6, 0x01, 0xBC, 0x00, 0xBB, 0xBF,
0x99, 0xF9, 0xBB, 0xAF;
stk500_devcode = 0x86;

avr910_devcode = 0x;

signature = 0x1e 0x95 0x0F;
pagel = 0xd7;
bs2 = 0xc2;
chip_erase_delay = 9000;
pgm_enable = "1 0 1 0 1 1 0 0 0 1 0 1 0 0 1 1",
"x x x x x x x x x x x x x x x x";

chip_erase = "1 0 1 0 1 1 0 0 1 0 0 x x x x x",
"x x x x x x x x x x x x x x x x";