If a SHM or PHC refclock has a very large offset compensated by the
offset option, or ignored with the pps or local option, there is a
persistent loss of precision in the calculation of the sample offset
using the double format.
Rework the code to delay the calculation of the accumulated offset to
include the specificed compensation and remaining correction of the
system clock, where the calculation can be split to improve the
precision. In the pps mode ignore integer seconds competely.
The precision of the SOCK refclock is now limited to 1 nanosecond due to
the extra double->timespec->double conversion.
It was never used for anything and messages in debug output already
include filenames, which can be easily grepped if there is a need
to see log messages only from a particular file.
Replace struct timeval with struct timespec as the main data type for
timestamps. This will allow the NTP code to work with timestamps in
nanosecond resolution.
