This is a problem I've seen at every company I've ever worked at. Everyone starts off thinking they'll have independence, but it's only natural to build on what already exists and thus you end up with complex dependency topologies.

Large software companies like Google/Facebook home build their own opinionated frameworks for publishing services that include citing of dependencies via config files. Internal engines then scrape for these configs and manage the relationship topology across environments. As far as SWEs are concerned its like magic.

I'm working on trying to standardize such a framework, https://docs.architect.io, and would love preliminary feedback.