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Update RTW to use new user configuration #3826

@ehogan

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@ehogan

Changes have been made to the user configuration since the last release (v2.11.0). The RTW now shows the following messages:

${HOME}/cylc-run/recipe_test_workflow/run2/share/lib/python/ESMValCore/esmvalcore/config/_config_object.py:619: ESMValCoreDeprecationWarning: Usage of the single configuration file ~/.esmvaltool/config-user.yml or specifying it via CLI argument `--config_file` has been deprecated in ESMValCore version 2.12.0 and is scheduled for removal in version 2.14.0. Please run `mkdir -p ~/.config/esmvaltool && mv ${HOME}/cylc-run/recipe_test_workflow/run2/share/cycle/20241128T0100Z/config-user.yml ~/.config/esmvaltool` (or alternatively use a custom `--config_dir`) and omit `--config_file`.
  config_obj.reload()
${HOME}/cylc-run/recipe_test_workflow/run2/share/lib/python/ESMValCore/esmvalcore/config/_config_validators.py:403: ESMValCoreDeprecationWarning: The configuration option or command line argument `config_file` has been deprecated in ESMValCore version 2.12.0 and is scheduled for removal in version 2.14.0. Please use the option `config_dir` instead.
  _handle_deprecation(option, deprecated_version, remove_version, more_info)
${HOME}/cylc-run/recipe_test_workflow/run2/share/lib/python/ESMValCore/esmvalcore/_main.py:421: ESMValCoreDeprecationWarning: The method `CFG.load_from_file()` has been deprecated in ESMValCore version 2.12.0 and is scheduled for removal in version 2.14.0. Please use `CFG.load_from_dirs()` instead.
  CFG.load_from_file(kwargs["config_file"])
${HOME}/cylc-run/recipe_test_workflow/run2/share/lib/python/ESMValCore/esmvalcore/config/_config_validators.py:403: ESMValCoreDeprecationWarning: The configuration option or command line argument `config_file` has been deprecated in ESMValCore version 2.12.0 and is scheduled for removal in version 2.14.0. Please use the option `config_dir` instead.
  _handle_deprecation(option, deprecated_version, remove_version, more_info)
${HOME}/cylc-run/recipe_test_workflow/run2/share/lib/python/ESMValCore/esmvalcore/config/_config_validators.py:403: ESMValCoreDeprecationWarning: The configuration option or command line argument `config_file` has been deprecated in ESMValCore version 2.12.0 and is scheduled for removal in version 2.14.0. Please use the option `config_dir` instead.
  _handle_deprecation(option, deprecated_version, remove_version, more_info)
${HOME}/cylc-run/recipe_test_workflow/run2/share/lib/python/ESMValCore/esmvalcore/config/_config_validators.py:403: ESMValCoreDeprecationWarning: The configuration option or command line argument `config_file` has been deprecated in ESMValCore version 2.12.0 and is scheduled for removal in version 2.14.0. Please use the option `config_dir` instead.
  _handle_deprecation(option, deprecated_version, remove_version, more_info)

The RTW should be updated to use the new configuration.

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