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In the C++ linker settings - if no linker option is set (be it a library, an option etc.), the 'additonal options' are not saved. This makes it impossible to only add a linker related command line to a project. Not sure if this is only OSX, as for now I can only observe it under this OS.
linux has this problem also
fixed: http://hg.netbeans.org/cnd-main/rev/8f0c5322a767
Integrated into 'main-golden', will be available in build *201004200200* on http://bits.netbeans.org/dev/nightly/ (upload may still be in progress) Changeset: http://hg.netbeans.org/main/rev/8f0c5322a767 User: Vladimir Voskresensky <vv159170@netbeans.org> Log: fixed #184384 - linker options not saved if no linker item set