I guess it depends on who should have access to them, but at the company I work for, we keep all the private config files backed up in a secure place (local network server, encrypted cloud storage, whatever) and the config files are added to .gitignore. This is especially important for databases with personal info.

We load all secrets in from an instance of Hashicorp Vault we have running.

It’s pretty easy API to use, has packages for most languages, has a solid docker image, and is compatible with pretty much every type of storage under the sun.

I think, and i could be wrong, but you should be storing them in a password manager style service, and then have your application pull them out.

Which is just commiting the keys with extra steps I guess :/