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.
If this migration has already been run and content has been published do we really want to remove the directory if the migration gets run again by some fluke?