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It's a lockfile. It signals that configuration is currently being applied, and so another run shouldn't be started. I believe it only contains a PID to allow Puppet to attempt to check whether it's actually valid - it checks that there is actually a process with that PID, in case the agent crashed and left the lockfile behind.
Unfortunately, I've found in the past (this may or may not still be true) that Puppet doesn't seem to validate the process name, so you can end up in a situation where (especially after a reboot if the lockfile persists) another process ends up using that PID, which causes Puppet never to run again.
Using $rundir (which should be defined somewhere that doesn't persist across reboots), as mentioned above, in the path to this lockfile has cured the problem in our case; that should only require changing the default.
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