[JENKINS-56403]: Renaming agents doesn't remove old agent configuration from disk

[JENKINS-33780] introduced a regression in persisting the update to disk.
In prior code, the update was performed through a full config save after
updating the nodes, but the functionality was not carried over.

* Added a file delete call to remove the old agent from disk iff
  the node name was changed.
* Add tests for this scenario and when node name was not updated.