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The issue is that the type of description_files node is a mgnl:contentNode and the default Rule allows only for mgnl:contentNode, mgnl:resource and mgnl:metaData (RuleBasedCommand.getRule()).
When versioning recursively, we reverse the rule to exclude children that have to be versioned on their own from those that need to be versioned with the current node (anonymouse ContentFilter in VersionCommand.versionRecursively()). This in turn excludes description_files node from the list of children that need to be versioned with its parent content node. Since the description_files node is not in the original list of nodes to be versioned either there is node missing by the end of versioning.
There might be actually two separate issues at play here as sometimes the message is .../description_files node is missing and sometimes the .../description_files/MetaData node is missing
While the above explanation of the issue might not be fully correct yet, issue is reproducible with clean installation of DMS 1.3 as well as with upgrade from previous versions and is likely related to the rules and node selection during versioning rather then to node type definition.
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