add bundle clean to upgrade docs
This MR adds a bundle clean after installing new gems. Bundle clean removes old, not needed gems to keep the system clean.
See merge request !2809
These sections were removed but:
- even if the NGINX config wasn't
modified, it might be in future updates so it's better to always have it
instead of having to remember to add it depending on the changes
- the init script update section must be there since it's a safe command
line that should be run on every update
[ci skip]
