Moved the jira apache2 config to a file ending .conf

Apache 2 on Ubuntu LTS 14.04 seems to need to be in a file ending in .conf to be detected by the a2ensite script.
Update for the new TSM location.

Also fixed another hyphen in variable as well.
Fix for the multiple mysql packages.

The hack we were using to install multiple packages stopped working with puppet 3 so simplify it.