Using a password manager for fetching them when needed. 1Password in my case, but I'm sure any password manager can be used for storing secrets for most programming projects.
Edit: Testing 1Password myself, with 1password desktop and shell, if I have authed myself once in shell, then "spawn" would be able to get all of my credentials from 1Password.
So I'm not actually sure how much better than plaintext is that. Unless you use service accounts there.
The approach also depends on the project. There is a bunch of different approaches and I don't think there is one approach that would work for every project, and sometimes I requires some wrangling but takes 5-10 minutes tops.
Some basic information about how you could make it work with 1Password: https://developer.1password.com/docs/cli/secrets-environment...