Comparing code on running servers

Is there a way of comparing code running on two Ensemble servers - ideally excluding certain types of difference?

We are a new team working in HealthCare (lots of HL7, some web-services). As well as doing new development on local servers with suitable source control, we have a large code base we've inherited from an external supplier for which we have no log of versions or differences. We have a live server and test server - and we've stumbled across a couple of places where there are differences in logic in addition to the expected differences in endpoints. Is there any way of systematically comparing the code running on those two servers, so we can identify all the differences? Eg a script to run against exports of the code created on the two servers that intelligently compares and highlights differences, but excludes things like differences in endpoints?