In my case, I have things like Github Personal Access Tokens stored in my password manager and then use chezmoi's templates to populate them in my dotfiles, for example:
This means that:
1. My secrets are safely stored in my password manager so I can share my dotfiles.
2. When I update the secret in my password manager it automatically gets updated in my dotfiles when I run `chezmoi apply`.
What secrets? I generally don’t copy them, but you could manually. For example I use the same ssh keypair on two machines, but I generally don’t.