If chronyc sent a request which caused chronyd to step the clock (e.g.
makestep, settime) and the second reading of the clock before calling
select() to wait for a response happened after the clock was stepped, a
new request could be sent immediately and chronyd would process the same
command twice. If the second request failed (e.g. a settime request too
close to the first request), chronyc would report an error.
Change the submit_request() function to read the clock only once per
select() to wait for the first response even when the clock was stepped.