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Product Version: NetBeans IDE Dev (Build 200708200000) Select Profile Project & Subproject Classes option as default for compound projects. It could be useful since availability of this option could be overseen by user and Profile Only Project Classes option could be expected to work as before (as Profile Project & Subproject Classes option).
*** Issue 116501 has been marked as a duplicate of this issue. ***
According to yardus' new issue, reclassifying it as DEFECT
Profile Only Project Classes instr. filter isn't available if the project doesn't have any java sources. Fixed for Beta2.