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 sidebar info.
Merge pull request #366 from laurenrother/pe3.3.1

Updates modules_publishing and modules_installing for PE 3.3.1 release