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Even if you have made no changes to a module X, after running ant -f nbbuild/build.xml -Dmodules= -Dfixedmodules=X merge you will see Copying 1 file to .../nbbuild/netbeans which is in fact X/netbeans/update_tracking/X.xml. To improve incremental builds, UT.write() should check if the file it is writing actually differs from the existing one (if any), and if so not do so (or put the timestamp back). However if update_tracking/*.xml are to be generated directly to nbbuild/netbeans (with redesigned build system) then it does not matter so much and this could be closed WONTFIX.
Setting WONTFIX per suggestion