global: check that secret_file is not already changed

In all commands, if the secret file in action has already been modified in the git repo, it will loose previous data and override the file

We should avoid this, and through an error

There are two cases which rises because of the secret file change in the local machine. Warn the user and stop the repo-cli in case of:

- [x] If secret file is staged with changes
- [x] If the local repo and the github master repo is not even.