Operation registries are overwritten by Nuxeo IDE

When updating the registry from Nuxeo IDE, currently, it overrides the Studio operation registry instead of appending to it, which is a problem when the customer has already declared manually some operations.

One solution could be to have a separate registry in Studio, or to "complete/update" propertly the existing one, based on the ids of the operations.

The user registry editable in Studio should override any other operations already declared in builtin registries or registries coming from the IDE.
Some validation warnings should be added to ease up detection of leftover contributions (in case they're added to builtin ones at some point for instance)