If your issue is that if you already have some changes to some files staged, and you have made subsequent changes to your working directory, if you git add . then it will not be possible to revert the cache to the state it was in before… well, yes, but there’s an easy way to checkpoint the state of the staged cache: git commit.
But to be clear: I’m the kind of person who runs git add .; that means I’m not maintaining a secret hidden third set of changes in the cache. I’m making changes in my working directory, and when those changes are in the shape I want them to be, I am staging all of those changes so I can commit all of those changes. If git add . overwrites a previous state of cached files, that’s fine - if I didn’t commit them I don’t want them.
Committing a codebase state that only exists in the cache and in your mind, on which you haven’t therefore run any build or test or linting tools because that precise set of changes has never existed in isolation in your codebase strikes me as requiring far too much mental powerlifting.
But to be clear: I’m the kind of person who runs git add .; that means I’m not maintaining a secret hidden third set of changes in the cache. I’m making changes in my working directory, and when those changes are in the shape I want them to be, I am staging all of those changes so I can commit all of those changes. If git add . overwrites a previous state of cached files, that’s fine - if I didn’t commit them I don’t want them.
Committing a codebase state that only exists in the cache and in your mind, on which you haven’t therefore run any build or test or linting tools because that precise set of changes has never existed in isolation in your codebase strikes me as requiring far too much mental powerlifting.