fix(path_utils): resolve C(E|T)SM root paths in Python tools (resolves #2658, #3552)

[johnpaulalex]

Description of changes

This PR resolves issues #2658 and #3552 where CTSM Python tools (gen_mksurfdata_namelist, subset_data, run_tower, tower_site) failed when executed inside a full CESM checkout layout (<CESM_ROOT>/components/clm).

Key Refactoring:

1. Added path_under_ctsm() & path_under_top_submodule():
   • path_under_ctsm() strictly resolves submodules under <CTSM_ROOT>/<submodule>.
   • path_under_top_submodule() checks <CTSM_ROOT>/<submodule> first, falling back to <CESM_ROOT>/<submodule> when inside a CESM checkout.
2. Added path_to_ccs_config() & path_to_top_root():
   • Replaced fragile relative path_to_cime()/../ccs_config calls in gen_mksurfdata_namelist with path_to_ccs_config().
   • Updated subset_data.py, run_tower.py, and tower_site.py to use path_to_top_root() for cesmroot while retaining path_to_ctsm_root() for CTSM-internal config (default_data_2000.cfg, cime_config/usermods_dirs).
3. Renamed standalone_only to ctsm_only:
   • Updated parameter names across path_utils.py, run_sys_tests, and unit test modules for clearer intent.
4. Targeted Unit Tests:
   • Added test_setupFiles_cesmCheckoutLayout in test_unit_subset_data.py.
   • Added test_towerSite_cesmCheckoutLayout in test_unit_run_tower.py.

Specific notes

Contributors other than yourself, if any:

• None

CTSM issues resolved or otherwise addressed, if any:

• Resolves mksurfdata_esmf FAILS in CESM checkouts; use CTSM instead #2658
• Resolves Make Python tools work in CESM checkout #3552

Description of generative AI usage:
Google Antigravity was used to write the code and tests, followed by human-guided verification.

Any user interface changes (namelist or namelist defaults changes)?
None.

Testing planned or performed, if any:

• python3 -m unittest python/ctsm/test/test_unit_path_utils.py: 15/15 OK
• python3 -m unittest python/ctsm/test/test_unit_subset_data.py: 37/37 OK (including test_setupFiles_cesmCheckoutLayout)
• python3 -m unittest python/ctsm/test/test_unit_run_tower.py: 3/3 OK (including test_towerSite_cesmCheckoutLayout)

Requirements before merge:

• I have followed the CTSM contribution guidelines.
• The code in this PR branch builds with no errors.
• The code in this PR branch runs with no errors. Briefly describe tested configuration(s): Python unit test suites (test_unit_path_utils.py, test_unit_subset_data.py, test_unit_run_tower.py) under macOS python3 environment.
• This either (a) does not change answers, (b) it only changes answers at roundoff level, or (c) I have performed a scientific evaluation of the answer changes. Which?: (a) Does not change answers (pure toolchain fix).
• I have reviewed relevant parts of the CLM documentation Tech Note or User's Guide to determine if anything needs to be changed or added. If it does, describe: No changes required.
• This PR either (a) does not create a need to update the documentation or (b) includes required documentation updates (see guidelines for contributing documentation). Which?: (a) Does not require documentation updates.