Start Xilinx ise according to the instructions (I used Release Version: 9.2.04.i Application Version: J. 40)
Select Project > Source Control > Import
For "Project file to import", browse to {EMC2}/src/hal/drivers/mesa-hostmot2/firmware/7i43/SOURCE/hostmot2_import.tcl
For "Directory to import to", select a new empty directory (you can create an empty one using the "folder with sparkle" icon)
Click OK
After a few moments the import process will complete.
To rebuild the FPGA firmware, choose Process > Implement Top Module. This will print many warnings and may take a long time, particularly on slow PCs -- several minutes on my 2.2GHz Core 2 Duo machine.
To build the BIT file, find the Processes tab. Double click "Generate Programming File".
Copy the i43hostmot2.bit file from the project directory to the location and name expected by the emc build process (src/hal/drivers/mesa7i43-firmware/???.bit); I am not sure what the naming convention is for these files.
To generate the firmware for the other size of FPGA chip, right click xc3s400 near the top of "sources" and choose "XC3S200" for Device. (If you're building for yourself, you need only build the one you want; If you're building for others, you must build all combinations)
1. First, and even before I decided to build the hostmot2 firmware, I installed the latest free version of the Xilinx software for 32 bit linux. To install this, you go to: http://www.xilinx.com/support/download/index.htm and download "Full Installer for Linux" The file I got was Xilinx_ISE_DS_Lin_14.4_P.49d.3.0.tar. They'll make you register for an account before you can do anything, so be prepared to tell them your life story :) This file is about 6-1/2 Gigabytes, so it'll take a while. Once you have the file, untar it and run 'xsetup'.
2. sudo apt-get install ghdl