Issue 1626 - Moves setup and constants to core, deprecates globals, __default_file__

[lsawade]

Description

• deprecates setup
• makes constants non config file
• deprecates globals unused

Issue Number

Closes #1626

Checklist

Please make sure to check developer documentation on specfem docs.

• I ran the code through pre-commit to check style
• THE DOCUMENTATION BUILDS WITHOUT WARNINGS/ERRORS
• I have added labels to the PR (see right hand side of the PR page)
• My code passes all the integration tests
• I have added sufficient unittests to test my changes
• I have added/updated documentation for the changes I am proposing
• I have updated CMakeLists to ensure my code builds
• My code builds across all platforms