@Douglas-Kryder
Hi guys. Thank you so much for your support. I've returned the Arduino dock and the new one works straight from the box. As stated above, it is not the first blown component I've bought from those guys. Someone brings a defective item back and they just put it back on the shelf. NEVER buying from them again.
Anyway, thanks allot. I really appreciate your support.

@György-Farkas
Ok, thank you so much. But I am confidant that the omega is working. The I2C port seems to be working as well. I think I should take the Arduino Dock 2 back for a refund. It might have been brought back by someone else who maybe blew it and those guys just put it back on the shelf. They are known for doing that. It is also not the first blown (and previously returned) component I bought from them. Is there anything I can check on the Arduino dock 2 side, to see if it is actually working. What happens is:

1. blue led solid on
2. when I load sketch through IDE it compiles, and the moment it wants to start loading it on the Atmega chip, the blue led goes off for a split second and comes back on, after which I get the error message, stating the the chip could not be detected.
   Can I read the I2C port of the arduino dock? I read address 0x08 but always get 0xff in return. The chip is either "empty" or not working at all. I'm trying to figure out if I should take it back since it's going to be a mission to get it swopped for a new one.

EDIT: The issue definitely is on the I2C between the Omega and Arduino dock.
If I read the value of the blue led with:

i2cget -y 0 0x08

I get:

0xff

and I should be getting 0x01 or 0x00
If I send a command to toggle the blue led (i2cset -y 0 0x08 0x00), the command executes with no errors but nothing changes on the Arduino dock.
Am I not missing a library or something on the Omega side?

@György-Farkas
Yes I realized that the tutorial was for the previous version of the Omega after I tried it, so I hope I didn't damage anything. I did install arduino-dock at first but then removed it and installed arduino-dock 2. However, the omega is working fine. Having said that, maybe following the tutorial damaged the I2C bus? But does it not have a level converter on that bus (and other pins) ?
EDIT: The OLed expansion still works on the omega. This means that the I2C is working right? If I try to read the OLed (0x3c), I get 0x03, so I assume that the "read" also works.

@Douglas-Kryder
Thank you. I did follow those steps to the T. The IDE picks up the Omega on the network etc. Is there a specific step that will cause that error?

@György-Farkas
Thank you for the reply. I tried to load the bootloader as discussed in "Arduino Dock Initial Setup"
https://wiki.onion.io/Tutorials/Arduino-Dock/Initial-Setup

@Douglas-Kryder
Thank you for your reply. Yes I'm positive, but the problem is not with the IDE. I tried to copy the hex file to the Omega2+ and load it using the terminal and am getting the same error. Also, if i read 0x08 from the ATmega I get 0xFF. I did not successfully load any bootloaders but tried to. I tried with the I2C and ICSP methods using the Expansion Dock 2, which both failed because the device (ATmega) could not be detected. I later read that loading the bootloader is actually not needed for the Arduino Dock 2. Starting to wonder if this one is defective maybe?

Please help me. I still cannot get the Arduino Dock 2 to flash a sketch. Have tried everything I could read and think of and still getting the same error:

avrdude: AVR device not responding
avrdude: initialization failed, rc=-1
Double check connections and try again, or use -F to override
this check.

@György-Farkas
Thank you. I have just removed Arduino 1.8.1 and installed 1.8.0 (and did the other steps), and I am still getting the same error. Did you load any bootloader to your Arduino Dock 2? I tried with both methods using the Expansion Dock, which also failed, but I read afterwards that it is not necessary with the Dock 2.

avrdude: AVR device not responding
avrdude: initialization failed, rc=-1
Double check connections and try again, or use -F to override
this check.

Hi,
I've been struggling for more than a week to get my Arduino Dock 2 working. I followed all the instructions and other tips but have no luck. The Arduino IDE connects to the Omega 2, but gives an error when the loading of the hex is supposed to start. I get the same error when loading with terminal.

Sketch uses 5092 bytes (15%) of program storage space. Maximum is 32256 bytes.
Global variables use 199 bytes (9%) of dynamic memory, leaving 1849 bytes for local variables. Maximum is 2048 bytes.

Flashing application '/tmp/sketch.hex' ...

ERROR, flash NOT successful
Flash complete!
avrdude: AVR device not responding
avrdude: initialization failed, rc=-1
Double check connections and try again, or use -F to override
this check.

The Omega 2+ has Ω-ware: 0.1.10 b160 and using avrdude_6.1-1
Staring to wonder if it's not easier to use a 3.3v Pic18 or Arduino on a separate board, but the Uno and Omega on the same board seems like a really neat and compact solution. Is it some versioning issue maybe? Please help me! Like I said it has been over a week. I'm not new to microcontrollers or linux.