[Certora] Use configuration files

[QGarchery]

The purpose of this PR is to use configuration files instead of bash scripts. The advantages are:

• it scopes the commands well, you cannot modify something else that would break the script (note that you can still wrap it with a script if necessary)
• it is more tightly integrated with the CLI, so you can add arguments more easily and get auto-completion notably
• it works with the certoraMutate tool too