The different timestamps are just when they were created locally, so I don't think they are out of sync as far as content. If you want to make the timestamps match, you could first do
mvn dependency:purge-local-repository
That should clear out your project dependencies from the local repo, and then you can download them again with the correct timestamps.
I'm not sure why maven doesn't download sources by default when they are available. Maybe because it would slow down the initial build a little bit if you just want to build and don't care about the sources.
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JBossMetaData.getEnterpriseBeans() should return a JBossEnterpriseBeansMetaData, which implements IEnterpriseBeansMetaData. For the raw parsing output this should be the jboss.xml contents. To create the merged view we do need to create a new JBossMetaData instance and merge the jboss and spec parse results, so we agree there.
In terms of having the override associated with the jboss version of the metadata, its not really needed and could be dropped. I do think we do need the merge logic between the spec and jboss classes in the various classes for ease of maintence. I don't have a strong prefernce for merging into this vs one of the arguments.
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The point of having the override is to allow for serializing the data back out to the original source(s).
NamedMetaDataWithDescriptionGroupWithOverride is for holding uniquely named jboss.xml data that applies to an override. I was trying various things to get the merged view, and ensureOverride is a hack I don't think should be used.
Your right, that merged.merge(...) usage is incorrect relative to the current merge method impls.
The standardjboss.xml case is a special case of a partial jboss.xml that is handled by the JBossMetaDataWrapper. I don't think we need another merge to support that.
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