Remove `stage()` and `execute()` from `MADABaseJobManager`

The `stage()` and `execute()` methods from `MADABaseJobManager` are from a super alpha version of this repository. There's been lots of changes since these were actually utilized and can now be replaced in favor of `submit_*()` commands.

Locate the MADABaseJobManager class and inspect its stage(), execute(), and submit_*() methods. Search for references to the obsolete methods before removing them; done means stage() and execute() are no longer part of the manager while the submit_*() commands remain the supported path.

Written by the indexing model from the issue text.