Updates modules_publishing and modules_installing for PE 3.3.1 release

PMT bug (JIRA PE-5074 and PE-5120) has been fixed. Remove publisher workaround steps. Update upgrading/uninstalling sections with --ignore-changes flag. Add pages specifically to PE docs. Add sidebar navigation for these pages.
Please change this "puppet.conf" link to the following:

`[`puppet.conf`](/puppet/3.6/reference/config_file_main.html)`

(I must have made that change to the 3.6 version of the file after you copied it to make this new version.)