Fix committed. The problem was related to an earlier change that I had made that will do a proper organize of imports including sorting and grouping. The problem was related to semi-colons being added by the ImportRewrite and then removed again through Groovy-Eclipse code.
In the end, I decided to copy 3 JDT classes into groovy eclipse code: ImportRewrite, ImportRewriteAnalyzer, and CodeStyleConfiguration. These classes are now stored in the jdt_src_patched source folder.
Now, semi-colons are never added and so, they do not need to be removed. Also, there is no extra whitespace added to the end of imports.
I also raised:
to figure out if/how something can be back-ported into JDT.