The FPGA1394_QLA subdirectory is the source code for the FPGA1394 board paired with the QLA. Currently, the QLA is the only supported companion board, but support for other boards could be added in different sub-directories. In that case, it would make sense to make a separate sub-directory for functionality on the FPGA1394 board, such as the FireWire interface, so that it can be shared between the different board configurations.
Note that there are two versions of the FPGA1394 board, Rev 1.x and Rev 2.x, where the latter version also contains an Ethernet interface. Thus, there are two main Verilog modules: FPGA1394_QLA.v (for Rev 1.x) and FPGA1394Eth_QLA.v (for Rev 2.x).
The project can be built using CMake and the Xilinx command line tools (preferred), or by loading one of the project files (FPGA1394-QLA.xise or FPGA1394Eth-QLA.xise) into Xilinx ISE. See the wiki build instructions.
Documentation for the firmware is on the wiki: https://github.com/jhu-cisst/mechatronics-firmware/wiki
For an overview of the boards and firmware, see: https://jhu-cisst.github.io/mechatronics/