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Likely already reported: when running the jaxb wizard, the generated classes are not picked up when invoking auto completion, or a search of classes in a dialog like "constructs jaxb object".
I am able to simulate in NB 6.1, Working in trunk 6.5. Attaching the patch which to fix in 6.1.
Created attachment 66516 [details] Patch for release61_fixes branch
Created attachment 66517 [details] Sources for changes files in patch for release61_fixes branch
Marking as fixed in 6.5.
This issue did not meet the criteria for inclusion in NetBeans 6.1 Patch 3.
Created attachment 66732 [details] Patch used to verify on top of 61fixes branch
Verified by copying the jar built using NB61 fixes branch to <NB61_Fixes_IDE>/java2/modules .
Justification for inclusion in patch: Code completion is important functionality for users using JAXB Wizard. Changes reasonable safe, adding additional lookup Query class needed by Code completion infrastructure, and refreshing FileSystem/FileObject after external process created the folder.
I've imported the attached changeset http://www.netbeans.org/nonav/issues/showattachment.cgi/66516/hg-patch-nb-issue-135917.txt into release61_fixes repository as http://hg.netbeans.org/release61_fixes/rev/c813dc0a67e6