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You should be able to right click on .aj files and select AspectJ Tools > Convert File Extension to .java However this entry is not currently appearing (the convert to .aj operation does appear for .java files).
This is because registering .aj as a java file extension (see bug 98547) causes CompilationUnits to be created for .aj files, instead of AJCompilationUnits, and the convert to .java action is currently defined in plugin.xml to only apply to AJCompilationUnits.
The change from bug 98547 has been reverted, so this problem has gone away. It would be possible to add the contribution with a *.aj name filter instead of using an instanceof test for AJCompilationUnits, but there doesn't seem to be anything to be gained from doing that now.