Remove star imports

[jasonb5]

Description

Removes wildcard (from ... import *) imports across the CIME Python codebase
and applies consistent PEP 8 import ordering to every file touched. Wildcard
imports hide a module's true dependencies, defeat static analysis, and let
unrelated symbols collide across modules.

Star imports removed (106 files)

• 97 files — replaced from CIME.XML.standard_module_setup import * with
  explicit imports
• 18 files — replaced from CIME.test_status import * with explicit imports
• 9 files appear in both groups
• from CIME.Tools.standard_script_setup import * in CIME/scripts/* is
  intentionally left in place (that module is the script bootstrap shim).

Import reordering (114 additional files)

Where imports were already explicit, the order was normalized to PEP 8 style:

1. import a, b, c collapsed to one module per line
2. Three groups separated by blank lines: stdlib → third-party → first-party (CIME)
3. Each group alphabetized
4. Symbols inside from X import (a, b, c) alphabetized

Backward compatibility preserved

• CIME/XML/standard_module_setup.py — marked DEPRECATED in the docstring;
  explicit imports tagged # noqa: F401 so external code that still does
  from CIME.XML.standard_module_setup import * (E3SM, CESM, NorESM
  cime_config/) continues to receive the same names.
• CIME/Tools/standard_script_setup.py — same treatment; also adds explicit
  re-exports of argparse and logging.

Totals

• 220 files changed
• +1,327 / −841 lines
• No tooling/config changes (no pyproject.toml, setup.cfg, or .isort.cfg
  modified)

Test status

Running pytest CIME/tests/ -k test_unit (with CIME_MACHINE=linux-generic,
E3SM cime_config/) yields 11 failed, 378 passed, 13 skipped. The same
11 failures reproduce identically on master and on the base branch
feat/refactor-core-foundation (PR #4982). They are pre-existing issues
unrelated to this PR — caused by E3SM machine-config / baseline mismatches
in the local test environment, not by import changes. Confirmed by running
the same suite on all three branches from clean worktrees.

Depends on: #4982

Checklist

• My code follows the style guidelines of this project (black formatting)
• I have performed a self-review of my own code
• My changes generate no new warnings
• I have added tests that exercise my feature/fix and existing tests continue to pass
• I have commented my code, particularly in hard-to-understand areas
• I have made corresponding additions and changes to the documentation

[github-actions]

You can preview documentation at https://esmci.github.io/cime/branch/fix/refactor-star-imports/html/index.html