For us, anything that would be a "secret" is stored in a SQLite database that sits next to the executable. In many cases, these secrets would additionally be encrypted with platform-specific techniques such as DPAPI. None of these databases are under source control and would be ignored upon commit.
If we want to load a secret into our application, we have to use an administrative web interface exposed by the application in each required environment. We view the management of secrets and other parameters as an important feature for our product and have built tooling up accordingly. Non-developers are able to manage secrets in our software, and we are actually trying to make this mandatory for compliance reasons.