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https://issues.apache.org/jira/browse/JCR-1660?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=12607166#action_12607166
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Jukka Zitting commented on JCR-1660:
------------------------------------

Yes, the rationale for this is that the consistency check is done within the 
scope of a single persistence manager, so it's not possible to check references 
to content within the shared or virtual jcr:system subtrees.

We could make the consistency check (and fix) feature more generic by moving it 
above the PersistenceManager interface. This way it could cover the shared and 
virtual subtrees and work for all persistence managers, not only for those that 
it has specifically been written for. There'd probably be a performance hit, 
but I think we could live with that as the check only happens when explicitly 
asked for.

> Consistency check / fix skips system nodes
> ------------------------------------------
>
>                 Key: JCR-1660
>                 URL: https://issues.apache.org/jira/browse/JCR-1660
>             Project: Jackrabbit
>          Issue Type: Bug
>          Components: jackrabbit-core
>            Reporter: Thomas Mueller
>            Priority: Minor
>
> BundleDbPersistenceManager.checkBundleConsistency skips the consistency check 
> and fix for some nodes:
> // skip check for system nodes (root, system root, version storage, node 
> types)
> if (entry.getId().toString().endsWith("babecafebabe")) {
>     continue;
> }
> if (id.toString().endsWith("babecafebabe")) {
>     continue;
> }
> The reason is (as far as I understand) that some system nodes refer to child 
> nodes in another workspace. But probably this check should be more specific 
> so that real inconsistencies in the system nodes are still fixed.
> Also, it is not nice to hardcode "babecafebabe" here: a constant should be 
> used, or some other solution that does not rely on a fixed system node id.

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