PART 2/3

LOADING or 'FLASHING'
With out final bitstream file in hand, we obviously want to shove it into an fpga. But how? For anyone who has programmed microcontrollers directly you know you need a box that lets your computer talk to the chip. For Arduino this is some SPI setup, but most FPGAs and ARM cores support JTAG (http://en.wikipedia.org/wiki/Joint_Test_Action_Group).
JTAG was intended as a method to do unit tests on highly complicated boards but its easily expandable architecture let people do what they wanted including programming their chips. Unfortunately each company implemented programming differently and while most companies produce chips that comply with JTAG signaling, each company and sometimes each chip handles programming their own way.
A new standard, IEEE 1532, was made to mitigate the damage of nonstandard interfaces. IEEE 1532 specified a format for people to write up the random nonstandard sequences required for chip configuration that can be interpreted and run, but sadly the standard suffers from common problems of Electrical Engineers writing specifications for software. The result is a standard too loose to really standardize anything, with tool writers often having to do custom work per chip using the chip's 1532 spec as a guideline.

CHALLENGES
In order to build tools for the TECHNOLOGY MAPPING, PLACE-AND-ROUTE, and BITSTREAM GENERATION steps, we need through documentation on the layout and configuration format of the FPGAs we are targeting. This information is unavailable and aggressively kept secret. One engineer bothered Xilinx until they told him that in order to receive the information his company would have to make them several million dollars a quarter, and even then he would only get it under an NDA. I have many opinions on how counter productive it is keeping this information secret and how it does not actually help Xilinx maintain competitiveness, but that is a different post.
The FPGA manufacturers are not only unhelpful, they do not want there to be open tools. I am not honestly sure why since Xilinx gives away their compiler for free. They do sell the professional version but Xilinx admitted that they only made several million from software sales and the cost of engineers writing it must have been in the same scale (they made 14 billion last year).
I would expect them to be indifferent to open tool chains but they actively work against tools that have been made. The licensing language in their compiler says you are not allowed to reverse engineer the tool (honestly not a big problem since the code is terrible), but you are also not allowed to look at the output bitstreams to try to figure anything out about the chip. If you think this is an idle threat, they have sent cease and desist letters to at least one tool chain that got pretty far reversing the bitstreams.
It is likely that this part of the license would lose if challenged in court, but as I said above, Xilinx made 14 billion last year, and no engineer has been able to challenge them even if they are right. I hope to get help from the EFF in the future to challenge and strike down this surprisingly common clause.

WHAT IS BEING DONE
Several of my friends on IRC cut FPGAs open and use high power optical microscopes as well as electron microscopes to capture each layer of the chip's layout. At least one is currently working on a computer vision tool to automatically map the chips and produce verilog code of the FPGAs themselves. If this works well we should be able to get enough information to build basic tools for each chip the whole process is applied to.