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Open some makefile and do some changes directly into the file on the disk. Now add some file under makefile node. Your "handmade" previous changes are rollbacked to the start state. Sources checked out 05/16/2001.
Fixed in cpplite/src/org/netbeans/modules/cpplite/MakefileNode.java in revision 1.6.
I hope this is really fixed in dev-2. Reopen this bug if it is not.