Puppet conf when using gem with /usr/local/etc/puppet name space

puppet.conf

[main]
  vardir=/var/puppet
  ssldir=$vardir/ssl
  #The default value is '$vardir/lib/facter:$vardir/facts'.

  rundir=/var/run/puppet
  logdir=/var/log/puppet

  confdir=/usr/local/etc/puppet
  templatedir=$confdir/templates
  
  factpath=$vardir/lib/facter

[master]
  # These are needed when the puppetmaster is run by passenger
  # and can safely be removed if webrick is used.
  # ssl_client_header = SSL_CLIENT_S_DN 
  # ssl_client_verify_header = SSL_CLIENT_VERIFY
  fileserverconfig = /usr/local/etc/puppet/fileserver.conf
  rest_authconfig = /usr/local/etc/puppet/auth.conf

[agent]
  # The file in which puppetd stores a list of the classes
  # associated with the retrieved configuratiion.  Can be loaded in
  # the separate ``puppet`` executable using the ``--loadclasses``
  # option.
  # The default value is '$confdir/classes.txt'.
  # classfile = $vardir/classes.txt

  # Where puppetd caches the local configuration.  An
  # extension indicating the cache format is added automatically.
  # The default value is '$confdir/localconfig'.
  # localconfig = $vardir/localconfig

  server=puppet

Choose [master] or [agent] not both..