I have new Vagrant Box with a recent installation of PE 3.1.3 and it fails 
the upgrade with the following error.

Complete!
Loaded plugins: fastestmirror, security
Cleaning repos: 
Cleaning up Everything
Cleaning up list of fastest mirrors
## Preserving existing puppet.conf for now...
## Preserving existing auth.conf
## Setting up puppet master...
Error: Could not intialize global default settings: Error converting value 
for param 'modulepath': Could not find value for $confdir
## Checking the agent certificate name detection...
!! ERROR: The agent certificate name was incorrect; please check that your 
system can correctly resolve its own FQDN
   in DNS.


 

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[main]
    certname = puppetmaster
    dns_alt_names = puppetmaster,puppet
    vardir = /var/opt/lib/pe-puppet
    logdir = /var/log/pe-puppet
    rundir = /var/run/pe-puppet
    modulepath = 
$confdir/modules:/etc/puppetlabs/puppet/modules:/opt/puppet/share/puppet/modules
    manifest = $confdir/manifests/unknown_environment.pp
    server = puppetmaster
    user  = pe-puppet
    group = pe-puppet
    archive_files = true
    archive_file_server = puppetmaster
    parser = future

[development]
  manifest = /puppet/env/development/manifests/site.pp
  modulepath = 
/puppet/env/development/modules:/$confdir/modules:/opt/puppet/share/puppet/modules
    

[production]
  manifest = /puppet/env/production/manifests/site.pp
  modulepath = 
/puppet/env/production/modules:/$confdir/modules:/opt/puppet/share/puppet/modules
    

[master]
    certname = puppetmaster
    ca_name = 'Puppet CA generated on puppetmaster.local at 2014-01-09 20:22:28 
+0000'
    reports = http,puppetdb
    reporturl = https://localhost:443/reports/upload
    node_terminus = exec
    external_nodes = /etc/puppetlabs/puppet-dashboard/external_node
    ssl_client_header = SSL_CLIENT_S_DN
    ssl_client_verify_header = SSL_CLIENT_VERIFY
    storeconfigs_backend = puppetdb
    storeconfigs = true

[agent]
    report = true
    classfile = $vardir/classes.txt
    localconfig = $vardir/localconfig
    graph = true
    pluginsync = true
    environment = production

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