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Sometimes I like to temporary replace a directory with JSPs in the maven target directory with a symlink back to the source. Then I can use a different editor, to quickly fix some issues in JSP. It seems that netbeans is detecting changes in the source and finds that it should copy it implicitly to the target. So far so good, but when using this symlink it will replace the JSP's in the source directory with empty files, which is pretty much the worst thing it can do in this situation, because it is very confusing and destructive.
*** This bug has been marked as a duplicate of bug 169962 ***