Don't use it as your main repository, that's all. Store your true history in another location, and use this as a way to reliably sync your files to the hosting

Don't use it as your main repository, that's all. Store your true history in another location, and use this as a way to reliably sync your files to the hosting environment. Setting up a CI environment with automated deploys is probably better, but this is great for small projects that don't warrant that level of configuration. Also, if you do go the CI route, this could just be how the final step of copying files works, rather than rsync or something.