...

<folderInfo id="nbeclipse.toolchain.nbl.rel.396284009." name="/" resourcePath="">
                    <toolChain id="nbeclipse.toolchain.nbl.rel.tc.1465290409" name="NetBurner Device Library" superClass="nbeclipse.toolchain.nbl.rel.tc">
                        <targetPlatform id="nbeclipse.toolchain.nbl.rel.tc.targetPlatform.283367649" isAbstract="false" name="NetBurner Module Library" superClass="nbeclipse.toolchain.nbl.rel.tc.targetPlatform"/>
                        <builder buildPath="${workspace_loc:/ITS8410_Lib/Release}" id="nbeclipse.toolchain.nbl.rel.tc.builder.2064025940" keepEnvironmentInBuildfile="false" managedBuildOn="true" name="Release ELF builder (MINGW)" superClass="nbeclipse.toolchain.nbl.rel.tc.builder"/>
                        <tool id="nbeclipse.toolchain.nbl.rel.tc.gcc.278195048" name="GNU C Compiler" superClass="nbeclipse.toolchain.nbl.rel.tc.gcc">
                            <inputType id="nbeclipse.toolchain.nbl.rel.tc.gcc.input.1060035859" name="GNU C Input" superClass="nbeclipse.toolchain.nbl.rel.tc.gcc.input"/>
                        </tool>
                        <tool id="nbeclipse.toolchain.nbl.rel.tc.gpp.767008127" name="GNU C++ Compiler" superClass="nbeclipse.toolchain.nbl.rel.tc.gpp">
                            <option id="nbeclipse.toolchain.super.gcc.directories.includepaths.1666029541" name="Include paths (-I)" superClass="nbeclipse.toolchain.super.gcc.directories.includepaths" valueType="includePath">
                                **inside here is an option list with all my include paths**
                    ...
                </folderInfo>

<folderInfo id="nbeclipse.toolchain.nbl.rel.396284009.2022231003" name="/" resourcePath="src">
                    <toolChain id="nbeclipse.toolchain.nbl.rel.tc.1982112905" name="NetBurner Device Library" superClass="nbeclipse.toolchain.nbl.rel.tc" unusedChildren="">
                        <targetPlatform id="nbeclipse.toolchain.nbl.rel.tc.targetPlatform" isAbstract="false" name="NetBurner Module Library" superClass="nbeclipse.toolchain.nbl.rel.tc.targetPlatform"/>
                        <tool id="nbeclipse.toolchain.nbl.rel.tc.gcc.1671008421" name="GNU C Compiler" superClass="nbeclipse.toolchain.nbl.rel.tc.gcc.278195048">
                            <inputType id="nbeclipse.toolchain.nbl.rel.tc.gcc.input.436341699" name="GNU C Input" superClass="nbeclipse.toolchain.nbl.rel.tc.gcc.input"/>
                        </tool>
                        <tool id="nbeclipse.toolchain.nbl.rel.tc.gpp.498310867" name="GNU C++ Compiler" superClass="nbeclipse.toolchain.nbl.rel.tc.gpp.767008127">

                            **the newly added paths don't show up here, if I add them manually things start working**

string strRunDir, strCurDir;
strRunDir = AfxGetApp()->m_pszExeName;
strCurDir = GetCurrentDirectory(...);