Hi,
I had similiar problem - I got SEVERE: Unable to load annotated class: ... error when in-place deployment under glassfish even when this class didn't exist in sources.
The solution that helped me was to shutdown netbeans and delete netbeans cache folder from disk (Windows: C:\Documents and Settings\yourUserName\.netbeans\6.9\var\cache)
The reason that problem occured was I had created this class with lower case first letter and had refactored it under netbeans to upper case first letter. After that during build netbeans created class file with lower case first letter (instead of upper case) in dist folder.
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