I don't to use any kind of serial communication, if I set DDRD = 0xFF this will disable the RXD line. Does this mean I won't be able to upload a program through the Arduino Bootloader?
Setting the pins as output only means something when the Arduino is running a sketch.
When a new sketch is to be uploaded, the Arduino is reset. The first thing that happens is that the bootloader looks to see if there is a new sketch to be uploaded. If so, the existing sketch is not run, but is replaced by the new one.
If not, the existing sketch begins executing again, and you can set all the pins again.
cool,
Thanks