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Improve 'praefect check' to handle NTP timeouts and proxies

Two problems recently noted with praefect check:

  1. NTP connections blocked by network firewalls will lead to confusing deadline exceeded errors, making it appear that the connection to the Gitaly node has failed
  2. HTTP proxies present in the shell running running the command but not the Praefect daemon's environment may lead to spurious connection failures
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