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Incorproate linkml-runtime, linkml-model/linkml-files.py changes from linkml-runtime#201

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Incorproate linkml-runtime, linkml-model/linkml-files.py changes from linkml-runtime#201
sierra-moxon wants to merge 6 commits into
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incorproate-linkmlfile-changes-from-linkml-runtime

fix tests according to changes in linkml-runtime: for consideration i…

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