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Hi Stephen --
The following seems to have worked for me at first blush. Pseudocode:
(a) Move a newer version of checkstyle-all-4.x.jar into bluej-extension-dir/checkstyle/
(b) In the checkstyle-extension source, edit 'config/manifest.mf'
so that "Class-Path" includes checkstyle/checkstyle-all-4.x.jar
(c) Then rebuild checkstyle-extension.jar ('ant -f build.xml build.bindist').
(d) Move your rebuilt checkstyle-extension.jar into the bluej-extension-dir