Clean-up and changes for 1.28 Gbps

MR includes various changes for going to 1.28 Gbps as a default:

• Minor fixes to eye diagram: Fix delay setting computation, flags for printing out raw error count values and skipping configuration step

• Added function for reading and setting just the virtual chip registers (used by the eye diagram script)

• Script for updating existing configs from 640 Mbps to 1.28 Gbps

• First draft of data merging check scripts (for both 4-to-1 and 2-to-1 data merging) - will likely need some tweaking, and implementation of a proper procedure for getting data merging to work, but for now return link quality for each chip, like:

• Update to documentation, clean up of the existing ones (specifically pcie and install), mention of eye diagram in the rd53a and rd53b pages, and dedicated guide for switching firmware.