Hi Scott,
I also have both Pis : model B and Pi2. They can write .hex files in Atmega, with or without bootloader. The 'gpio' programmer makes bit-banging on 4 serial lines, simply flashing an .hex file. You can afterwards use the bootloader with an ordinary serial interface, but with little or no interest as you're obliged to have the previous programmer to flash the bootloader the first time.
If the lock bits are set, only 'parallel' programmers can reset the device. In all other cases you can re-flash the fuses.
Out of factory the Atmega are configured with internal RC oscillator. You can then put the device on a breadboard without any crystal circuit. If you then configure the fuses to crystal oscillator, further programming will require the crystal on the breadboard (or on the target board if you're using ISP).
Denis
@Tom and @Denis
Guys,
I was finally able to sit down today and set up my new Pi2, I also bought a "build you own" UNO kit that was clearance at the local electronics store for $3. I bought it because I thought it would be fun to solder together and also it didn't have a programming FTDI or any programming chip on it. So I thought it would be a good test platform to try using Pi AVRDude with.
All went well, I have not programmed anything yet, but I was able to read the AVR and current locks.
Next I want to breadboard it, then use the dev PCB I found and set it up so I can change chips from the 328/128 to AtTiny chips with a couple of changes to some jumpers and use a ZIF DIP socket to be a little easier. I wanted to thank you for your input and help.
Now I just need to figure out what commands to use to make a backup hex file of a chip, assuming it may need some lock bits changed first, then backed up.
Oh, and now I can pull my component tester 328 and plug it into this uno board and flash it with the v1.18.
My friend got his today also, it's a SMD 328P, but his also has a 10 pin program header on the board. His firmware won't even let him bring up a menu to see what version it's currently running. So I think I will update his also after I check pins 6 and the other for contrast to the display to make sure it won't short out. If it's wired we may cut the traces and then update the firmware, but I need to get a closer look at it first to be sure.
Thanks again for the help guys,
Scott