ApolloCMFPGA updates regarding Firefly/GTY mapping to Quads.

Building firefly+polarity maps. YAML files containing firefly+channel indices (and GTY for FPGA-FPGA connections) mapped to quads with traces. Also have clocking information, n/p diff pair information, and the channel in the quad it is mapped to. Corresponding accessor functions for trace polarities and the firefly information based off rx/tx. Made a dummy command dumpFFInfo that dumps all the registered FF/GTY names with their corresponding channels that are registered in Herd.