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Update gflags, glog and jsoncpp to newer versions.
In addition to refreshing the gflags, glog and jsoncpp libraries, update the agent Makefile to run static_def_gen.py using `python3` instead of `python`. PiperOrigin-RevId: 461606067 Change-Id: If534897c75c804282913c75d34f6fdead7e373f7
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