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Every puppet run starts from a default manifest. With puppet apply, this is either the value of the manifest setting (usually /etc/puppet/manifests/site.pp) or the value you supply on the command line. The default manifest is ignored if you use the -e flag, or pipe into apply from stdin.

With master/agent Puppet, the master uses the manifest setting from the [master] configuration block, or the setting specified in your environment if you're using directory environments. On a vanilla installation of Puppet, the master checks /etc/puppet/manifests/site.pp. Any other manifest in that directory is ignored unless explicitly imported (a deprecated feature.)