Git: keep ignored files when switching branches

Question

I know it seems like a duplicate of GIT: How to keep ignored files when switching branches?, but I couldn't find my answer there.

So I created a new branch with the --orphan flag, to delete the commit history. Then I did git rm --cached on all the files, modified .gitignore to ignore some of them, then added and committed. As expected, the ignored files are not in the new repo (nor in any of its history). However, they disappear when I switch branches (that is, when I check out an old branch, then check out the new one again). How can I avoid that?

EDIT: The purpose of the whole operation was to prepare a project to be published on GitHub, so I wanted to hide some config files that contain private information like passwords, keys, etc. That's why I deleted the commit history by creating a new orphan branch. I understand that probably committing the files before adding them to .gitignore would solve the disappearing issue, but that would make the files ultimately visible in the public history. I tried to do git add -f, then git rm --cached, but it doesn't do the trick.

Answer 1

However, they disappear when I switch branches (that is, when I check out an old branch, then check out the new one again). How can I avoid that?

You cannot. This is by-design. In your publish branch, you do not have the files tracked, and you have a .gitignore for them. Great! But when you switch to some other branch that does have those files tracked, they will be checked out to your working directory. This is because a .gitignore only applies to untracked files.

From the documentation:

A gitignore file specifies intentionally untracked files that Git should ignore. Files already tracked by Git are not affected.

Now if you try to switch back to your publish branch, the files will be removed on-disk because they do not exist in that branch. Your .gitignore for these files is ignored because they are tracked and it would not apply to them.

(Note that they are - by definition - tracked even if they're in the branch that you're switching away from. This is mostly just an implementation detail and I concede that this may not be intuitive.)

What you want to do is remove every occurrence of these files in all the branches. Use a tool like BFG Repo Cleaner to remove these files from your history completely, in all branches. Then you can safely .gitignore them, then once they're gone completely you can safely push this to GitHub.