[jacob-moore22]

Description

Simplifies fierro::Logger and removes unused #includes across the multiphysics app.

Logger (common/include/logger.hpp, new common/src/logger.cpp)

• Rewrote the 950-line header-only logger as a ~95-line header plus a small .cpp. Removed the GPU-kernel logging path, which nothing used (Handle, FLOG_DEV, log_handle(), device ring buffers, StdoutTarget, all_ranks(), set_file_prefix). The header no longer includes Kokkos.
• Log levels are unchanged: Trace < Debug < Info < Warn < Error < Off, with trace/debug/info/warn/error, log(lvl, ...), set_level() and level().
• Uses printf-style C varargs with __attribute__((format(printf, ...))), so call sites now get compile-time format checking. This fixes the clang -Wformat-security warnings that came from the old logger.hpp:418.
• MPI: rank and size are read once in the constructor. Each rank writes to Fierro_log_<rank>, and rank 0 also writes to stdout. Lines are tagged [rank N][LEVEL]. flush() is no longer collective, so it is safe in loops whose trip count differs between ranks.
• Solver::log_handle() is removed. Solver::log and set_logger are unchanged, and no info/error/flush call sites changed.

Header cleanup

• Removed 106 unused #includes from 36 files. The candidates came from clang-include-cleaner. Removals that were only safe through transitive includes were put back, and every matar.h/ELEMENTS.h include was kept.
• Removed the unused logger.hpp include from region_fill.hpp.

Behavior notes

• Rank 0's terminal output now appears when each line is logged, instead of at the next flush(). The content and order are the same.
• Messages are no longer truncated at 512 bytes.
• This removes public logger API (listed above) that nothing in the tree uses. Any out-of-tree code that used it will need updating.

No new dependencies.

Type of change

Please select all relevant options

• Bug fix (non-breaking change which fixes an issue)
• Formatting and/or style fixes
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• This change requires a documentation update

How Has This Been Tested?

• Test A: Full rebuild of Fierro, then regression_tests/test_refactor.py against build/app/Fierro. 35/35 tests pass, and the results match the pre-change baseline.
• Test B: Ran an SGH 3D case with mpirun -np 1 and -np 4 (--oversubscribe).
  • Fierro_log_0..3 are created with each rank's lines, and only rank 0 prints to stdout.
  • The run exits cleanly with no hang.
  • Calling set_level(LogLevel::Warn) hides info lines while warn and error lines still print.
• Test C: Compiled each of the 17 headers that lost includes on its own, to confirm none of them relies on an include that was removed.

Not yet tested: clang/Apple clang, CUDA/HIP builds, and the regression suite on more than one rank.

Test Configuration:

• OS version: Fedora Linux 43 (kernel 7.1.12)
• Hardware: AMD Ryzen AI 9 HX 370 (24 threads), CPU only
• Compiler: GCC 15.3.1, Open MPI 5.0.8, Kokkos OpenMP + Serial backends

Checklist:

• My code follows the style guidelines of this project
• I have performed a self-review of my code
• I have commented my code, particularly in hard-to-understand areas
• I have made corresponding changes to the documentation
• My changes generate no new warnings
• The code builds from scratch with my new changes
• I have added tests that prove my fix is effective or that my feature works
• New and existing unit tests pass locally with my changes
• Any dependent changes have been merged and published in downstream modules