1153072 - do not delete /var/www/pulp_puppet on upgrade

Previously, the upgrade script would attempt to delete `/var/www/pulp_puppet`
as part of the upgrade procedure. This does not work since the upgrade runs as
apache user and not root.

Instead, simply copy the contents of the directory to the new location and add
a release note for users to remove the directory on their own.

Also, the migration script had an unrelated bug where **os.rmdir()** was being
used instead of **shutil.rmtree()**. This has been corrected.
We might not have permission to delete the original directory but we should be able to empty it's contents.