I have a $HOME/.gitignore that I use for this. (You can configure git to use that globally.) It's not a panacea, and I think other commenters are right that you

I have a $HOME/.gitignore that I use for this. (You can configure git to use that globally.) It's not a panacea, and I think other commenters are right that you should instead endeavor to organize things so that the project's own gitignore results in a sane workflow. But I think having permanently unstaged changes is worse.