Minor config documentation enhancements

[bgruening]

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[martenson]

the last commit here (7264a82) remove the user_config_templates_index_by option from the generated documents. It has already been missing from the schema, so I assume only the regeneration was behind. However it is still explicitly used in this test: https://github.com/galaxyproject/galaxy/blob/dev/test/unit/app/managers/test_user_file_sources.py#L591

Most likely a dead code line?