I found two methods that work on the Ubuntu Mate Platform. I worked into the lonely hours from sunset to sunrise.
(1) First method - I needed a programmer and I was aware of using Raspberry Pi 3 by BITBANGing the GPIO lines to the AVR like atmega328p. The trick is to use the hex file created from the Arduino IDE.
Program an AVR or Arduino Using Raspberry Pi GPIO
(2) Second method depends on having a programmer so I'll use method (1) above. To create the hex file without using the Arduino IDE, I'll try using the text "Make: AVR Programming" by Elliot Williams but this is much more difficult than method (1). On the other hand using method (2) is what the AVR professionals use when programming the chips...like Atmel Studio 7.
I was hoping that there was a AVR community here at this forum.
Jesse Mage
Addendum:
I tried working with the Raspbian Jessie OS but the communication protocols like I2C (TWI), SPI and more importantly Serial (UART) kept failing between the Raspberry Pi 3 and the Atmel Chips or even the Arduino boards. This is bad so here I am to see whether the Ubuntu Mate is more stable.
BUMPED TO A NEW TOPIC "AVR Programming"