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Fix Makefile for single flavor projects, ease timing in DAQ, fix csc_apex top file, fix IC controller output port

Evaldas Juska requested to merge top-ui-dev into devel
  • update Makefile to include flavor argument to generate_registers in all projects
  • fix csc_apex top file
  • fix in GBT IC controller (had been using reading output port)
  • add a register stage at the output of vfat_input_serializer to ease timing. Note: an improvement on clk40 and clk80 skew could be done by using BUFGCE_DIV to divide the clocks instead of MMCM
  • update regtools to print arguments it was called with

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