service: Standardize validation of Repository existence

Majority of RPCs in the commit package require Repository parameter to be passed. Some methods don't check if it is actually passed or not, in others the validation error is different in different RPC. We try to standardize the approach we use and fix all inconsistencies. All RPCs that rely on Repository parameter check the existence of it and return pre-defined error in case if it is missing.

Closes: #3717 (closed)