Copy additional xml files to clone

[jedwards4b]

Copy any additional xml files located in case into a case clone.

Test suite:
Test baseline:
Test namelist changes:
Test status: [bit for bit, roundoff, climate changing]

Fixes ESMCI#4794

User interface changes?:

Update gh-pages html (Y/N)?:

Code review:

[Copilot]

Pull Request Overview

This PR introduces a large set of new files and modules that extend the functionality of CIME. The new changes include:

• New XML interfaces and utilities (e.g. batch, archive, and various XML converters) that support additional configuration file handling and version conversion.
• A host of new command‐line tools under CIME/Tools for querying, comparing, validating, and processing XML data, testing, provenance, and workflow generation.

Reviewed Changes

Copilot reviewed 112 out of 2201 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
CIME/XML/batch.py	Implements the batch XML interface with support for appending additional XML files.
CIME/XML/archive_base.py	Introduces a base class for archive file handling with new helper methods.
CIME/XML/archive.py	Defines an Archive class that inherits from ArchiveBase to manage archive.xml files.
CIME/Tools/xmltestentry	Minor update: removed an extraneous newline from the test entry script.
CIME/Tools/xmlquery	Adds a comprehensive tool for querying variables in env_*xml files with various qualifiers.
CIME/Tools/xmlconvertors/grid_xml_converter.py	Provides grid XML conversion utilities from CIME2 to CIME5; note use of getchildren() below.
CIME/Tools/convert-grid-v1-to-v2	Implements conversion of grid XML files from version 1 to version 2 format.
CIME/Tools/xmlconvertors/config_pes_converter.py	Adds a tool for converting config_pes XML files from CIME2 format to CIME5.
CIME/Tools/xmlchange	Introduces a tool for updating variables in env_*xml files with comprehensive CLI options.
CIME/Tools/wait_for_tests	Implements a script to wait for queued tests to finish based on TestStatus files.
CIME/Tools/testreporter	New script to populate the CESM test database with test results.
CIME/Tools/standard_script_setup.py	Provides a standard setup for logging and importing utilities needed by all scripts.
CIME/Tools/simple_compare	Implements file comparison in a normalized way for non-namelist file diffing.
CIME/Tools/pelayout	Offers a utility to view and modify the PE layout of a case.
CIME/Tools/normalize_cases	Adds a tool to normalize a case directory by replacing test-ids, timestamps, and CIMEROOT.
CIME/Tools/mvsource	Provides a tool to update source file links when a case or CIMEROOT is moved.
CIME/Tools/mkSrcfiles	Perl script that generates a Srcfiles list of source code files in the case.
CIME/Tools/mkDepends	Updates dependency file generation in a more modern loop construct.
CIME/Tools/list_e3sm_tests	Introduces a script to list available E3SM test suites and specific test terms.
CIME/Tools/jenkins_generic_job	Implements a Jenkins wrapper job for running tests, cleaning up results, and dashboard updates.
CIME/Tools/get_standard_makefile_args	Outputs the standard makefile arguments for non-Python builds.
CIME/Tools/get_case_env	Dumps the CIME environment for a case; useful for shell integration.
CIME/Tools/getTiming	Provides a tool to extract timing information from a run.
CIME/Tools/generate_cylc_workflow.py	Generates a cylc workflow file for case submission automation.
CIME/Tools/e3sm_check_env	Checks that the system environment meets E3SM’s software requirements.
CIME/Tools/cs.status	Lists test results from TestStatus files with options for summary and failure counting.
CIME/Tools/component_generate_baseline	Generates and copies component history files as new baselines.
CIME/Tools/component_compare_test	Compares two component history files in a test case.
CIME/Tools/component_compare_copy	Copies the most recent history files with an appended suffix as backups.
CIME/Tools/component_compare_baseline	Compares current component history files against stored baselines.
CIME/Tools/compare_test_results	Analyzes test results quickly for non–bit‑for‑bit changes.
CIME/Tools/compare_namelists	Compares namelist files while ignoring order and insignificant whitespace differences.
CIME/Tools/code_checker	Checks that all CIME Python files are free of syntax errors and comply with PEP8 standards.

[Copilot]

The method getchildren() is deprecated in recent versions of Python's ElementTree. Consider replacing it with list(xmlnode) to ensure future compatibility.

Suggested change

	for child in xmlnode.getchildren():
	for child in list(xmlnode):