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cpplite.Utils does incorrect things with FileSystem.getSystemName. Remember that the system name is arbitrary and need not correspond to any file name. Use FileUtil.toFile etc. if you need to convert between File and FileObject.
It should be fixed by this commit: /usr/local/tigris/data/helm/cvs/repository/cpplite/src/org/netbeans/modules/cpplite/Utils.java,v <-- Utils.java new revision: 1.6; previous revision: 1.5
Actually upon looking at the source for Utils.java I would guess you really want to be using FileUtil.toFile and FileUtil.fromFile which are the official ways of converting FileObject <-> File; better to use the central impl than do it yourself.
So, I can not use proposed methods, as CPPLite should be compatible with release 3.2 (openide version 1.2.1) (ASAIK these methods were added in 1.29). But maybe I should copy&paste content of these methods (if they do not use any openide-private methods).
If you are trying to keep release32 compatibility, forget about it; it is not important. Copying and pasting will probably not help in release32.