add cleanup section to 5.0 upgrade guide

Add cleanup details to upgrade guide as gitolite and more is no longer used.
All in `home/git` which you can confirm via https://github.com/gitlabhq/gitlabhq/blob/4-2-stable/doc/install/installation.md & https://github.com/gitlabhq/gitlabhq/blob/4-2-stable/doc/install/structure.md.

`-rf` would likely be sufficient however I was looking to use the least arguments necessary.