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Problems with large numbers of Git files created by filesync module

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Recently our dev puppet master ran out of inodes - the culprit was the git files used internally by the filesync module (in turn used by Code Manager). We had over a million files in /opt/puppetlabs/server/data/puppetserver/filesync and these used up all the inodes, and these had reached this number over a period of about 2 weeks. Unsurprisingly this caused a few things to break, so I emptied the directory and restarted everything to get back up and running. Background: This is a shared server pulling code from Git via code manager, used by multiple teams. In the absence of a Git Hook to trigger the code manager deployment, we have a script running regularly to run the "puppet-code deploy" commands. At the time of the inode problem it was running every minute (so code pushed to Git would almost instantly appear on the host). I have now moved the cron script to every 15 mins but I'm just delaying the inevitable. And if I remove them while the server is up, puppet server crashes. Is there a way to prevent filesync from creating so many files, or a process I can use to clear them periodically without causing problems with code manager & puppet server? Version here is 2016.1

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