Removing defunct flags CORE and REACTOR

[john-science]

What is the change?

Here I removed two flags that are barely used and are definitely unnecessary.

Why is the change being made?

To close #1833

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Checklist

• This PR has only one purpose or idea.
• Tests have been added/updated to verify any new/changed code.

• The code style follows good practices.
• The commit message(s) follow good practices.

• The release notes have been updated if necessary.
• The documentation is still up-to-date in the doc folder.
• The dependencies are still up-to-date in pyproject.toml.