Replace manage_externals with git-fleximod

[nusbaume]

Originator(s): nusbaume Date: July 7th, 2024 One-line Summary: Replace manage_externals with git-fleximod

Purpose of changes:

This PR removes the manage_externals tool and replaces it with the new git-fleximod system, which is what will be used in CAM7 and CESM3. This PR also introduces an SE-CSLAM dycore build test to the CAM-SIMA regression test list.

Issues closed (include Github closing keyword and issue number):

Closes #266 Closes #275

Describe any changes made to build system:

Externals are now brought in via bin/git-fleximod update instead of manage_externals/checkout_externals.

Describe any changes made to the namelist: None

List any changes to the defaults for the boundary datasets: None

Describe any substantial timing or memory changes: None

Code reviewed by: cacraigucar, peverwhee

List all files eliminated:

D Externals.cfg D Externals_CAM.cfg D manage_externals/*

• Remove manage_externals tool and associated files

List all files added and what they do:

A .gitmodules A bin/git-fleximod A .lib/git-fleximod/* A external git submodules

• Add git-fleximod tool and associated files and submodules.

A cime_config/testdefs/testmods_dirs/cam/outfrq_kessler_se_cslam_derecho_nooutput/shell_commands A cime_config/testdefs/testmods_dirs/cam/outfrq_kessler_se_cslam_derecho_nooutput/user_nl_cam

• Add new SE-CSLAM dycore build test to regression test list.

List all existing files that have been modified, and describe the changes:

M .github/workflows/python_unit_tests.yml

• Use git-fleximod instead of manage_externals in testing workflow.

M .github/scripts/pr_mod_file_tests.py

• Ignore git-fleximod files when performing static analysis.

M .gitignore

• Update .gitignore to properly work with git submodules

M cime_config/cam_autogen.py

• Fix failing doctest

M cime_config/testdefs/testlist_cam.xml

• Add SE-CSLAM build test to regression test list.

Test results:

derecho/intel: All tests passed.

derehco/gnu: All tests passed, including snapshot tests for Kessler and Held-Suarez