Overall rules to go with seems to be

 # required for pps initialization
 capability dac_read_search,
 capability sys_time,
 /sys/devices/virtual/pps/ r,
 # to submit data to chrony
 ptrace read peer=/usr/sbin/chronyd,
 # for libusb
 /sys/devices/**/usb[0-9]*/** r,
 # triggered on fusercount, not strictly required and unsafe to allow
 # adding a denial rule silences the warnings
 deny ptrace read peer=unconfined,

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https://bugs.launchpad.net/bugs/1872175

Title:
  gpsd unable to open chrony PPS socket

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