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Updated ApolloCMFPGA to most recent emp-herd requirements

Gianfranco De Castro requested to merge cms-tracker-phase2-onlinesw/apollo-herd:feature/Serenity into master

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.

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