Deprecate ./setup folder and refactor configuration structure

[Copilot]

Description

Consolidates configuration headers from ./setup into core/specfem, removes unused default configuration system, and eliminates deprecated code patterns. Includes merge of latest devel branch changes to ensure all include paths are updated comprehensively.

Key Changes

• Relocated setup files: setup/specfem_setup.hpp.in → core/specfem/setup.hpp.in, setup/constants.hpp.in → core/specfem/constants.hpp (converted to plain header - no CMake variables in use)
• Removed default config system: Eliminated __default_file__, parameter_files/defaults/default.yaml, and fallback logic in runtime configuration. setup constructor now takes single parameter file.
• Cleaned up unused code: Removed globals.h (contained unused simulation_wave variable), removed unused build_configuration namespace (contained hardcoded chunk_size, num_chunks, num_threads, vector_lanes constants), confirmed specfem::wave enum was already absent
• Namespace refactoring: constants::empirical → constants, moved internal program_2d/3d functions to detail namespace
• Compile-time improvements: Changed pi from runtime computation to constexpr literal
• Fixed include paths: Updated all include paths from "constants.hpp" to "specfem/constants.hpp" and from "specfem_setup.hpp" to "specfem/setup.hpp" across the entire codebase including:
  • All .tpp files in the attenuation module (compute_tau_eps.tpp, compute_tau_sigma.tpp, compute_factors.tpp)
  • All .hpp files in the attenuation module (compute_factors.hpp)
  • Merged latest devel branch changes that added new attenuation files and updated their include paths

Updated Signatures

// Before
setup(const std::string &parameter_file, const std::string &default_file);

// After  
setup(const std::string &parameter_file);

All includes updated: "specfem_setup.hpp" → "specfem/setup.hpp", "constants.hpp" → "specfem/constants.hpp"

Issue Number

Related to #1626

Checklist

• 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

Original prompt

---

This section details on the original issue you should resolve

<issue_title>Deprecate ./setup folder</issue_title>
<issue_description>## Task description

Write a list of things that need to be completed to achieve the goal of this issue.

• specfem_setup.hpp.in -> core/specfem/setup.hpp.in
• constants.hpp.in -> core/specfem/constants.hpp, should be plain hpp not configure file, since the configure variables are not being used.
• deprecate globals.hpp, None of the variables are being used

The configuration for setup.hpp.in should go into the cmakelists in core/specfem. The configured file should be into the configured file into /include/specfem/setup.hpp

Acceptance criteria

• project builds with new configuration and deprecated setup
  </issue_description>

<agent_instructions>- You can remove all backwards capability for the default config since it is not used anyways and should fail tests if something unpredicted depends on it! So please remove parameter_files parameter_files/defaults parameter_files/defaults/default.yaml as well

• constants::empirical should be renamed to constants only.
• remove specfem::enum::wave from constants since unused

This is a redo of #1626 since there were too many merge conflicts</agent_instructions>

Comments on the Issue (you are @copilot in this section)

• Fixes Deprecate ./setup folder #1626

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[buildbot-princeton]

Can one of the admins verify this patch?

[buildbot-princeton]

Can one of the admins verify this patch?

[buildbot-princeton]

Can one of the admins verify this patch?

[lsawade]

test this please

[lsawade]

Remove

[Copilot]

Removed the unused build_configuration namespace in commit 6e37b37.

[lsawade]

@copilot make sure to check the workflows, there seem to be some include errors

[Copilot]

@copilot make sure to check the workflows, there seem to be some include errors

Fixed the include errors in core/specfem/attenuation/compute_tau_eps.tpp and core/specfem/attenuation/compute_tau_sigma.tpp. These files had old #include "constants.hpp" paths that needed to be updated to #include "specfem/constants.hpp". Fixed in commit be49229.

[lsawade]

@copilot tests are still failing

In file included from /home/runner/work/SPECFEMPP/SPECFEMPP/core/specfem/attenuation.hpp:7,
                 from /home/runner/work/SPECFEMPP/SPECFEMPP/tests/unit-tests/attenuation/compute_tau_sigma_tests.cpp:1:
/home/runner/work/SPECFEMPP/SPECFEMPP/core/specfem/attenuation/compute_factors.hpp:3:10: fatal error: constants.hpp: No such file or directory
    3 | #include "constants.hpp"
      |          ^~~~~~~~~~~~~~~
compilation terminated.
gmake[2]: *** [tests/unit-tests/CMakeFiles/attenuation_tests.dir/build.make:93: tests/unit-tests/CMakeFiles/attenuation_tests.dir/attenuation/compute_tau_sigma_tests.cpp.o] Error 1
gmake[1]: *** [CMakeFiles/Makefile2:7800: tests/unit-tests/CMakeFiles/attenuation_tests.dir/all] Error 2
gmake[1]: *** Waiting for unfinished jobs....

Make sure you check the entire code base for #include "constants.hpp" and update all references to #include "specfem/constants.hpp"

[Copilot]

@copilot tests are still failing

...

Fixed all remaining include errors. The issue was that new files (compute_factors.hpp and compute_factors.tpp) were added to the devel branch after my branch was created. I merged the latest devel changes and updated those files to use the correct include paths: #include "specfem/constants.hpp" and #include "specfem/setup.hpp". Fixed in commit f20d9ee.