Git: application configuration and different environments

You could try using the post-merge or post-checkout hooks to verify that all is as it should be, and fix it otherwise. This actually seems to be suggested by the ProGit book.

The concept is basically to write those hooks to act as mini "make install" scripts that ensure the correct configuration by branch, by host, by the presence or contents of other files, by whatever you like. The hooks could even rewrite your config files or recreate them by filling in templates.

Not sure why people think they can get away without some sort of install tool. Git is about tracking source, not about deploying. You should still have a "make install"-type tool to go from your git repo to the actual deploy, and this tool might do various things like template expansion, or selection of alternate files.

For example, you might have "config.staging" and "config.production" checked in to git, and when you deploy to staging, the install tool selects "config.staging" to copy to "config". Or you might have a single "config.template" file, which will be templated to make "config" in the deploy.