My coding in the past has always been very casual--I would grab a project from GitHub (or wherever) and implement it on my website if I liked it and I would just manually tweak it if I needed or wanted to, just making a note of the changes I made in case I ever needed to reinstall. I'm now getting deeper into development, however, and I have a GitHub repository that I develop on my Windows 8.1 machine and implement on three different "live" testing, non-critical environments that each require a different custom setup.
I've never used git in this way before with one live environment, let alone three. Is there an automated way to handle this with git, or do I have to stick with .gitignore and manually apply settings from ignored files? This question does mention GitHub because that's what I'm using, but any generalized answer that still gets at the premise of the question is acceptable.
If your issue is that you want each machine to read different configurations, you could set the config file to determine which system it is on and then have it load the corresponding settings.
Alternatively, if you do not have to change the structure of the config files, you could put them in some include path outside the git repo.