Update run-qmake template to run Orbit configure.py first, followed by mkspec export. This should allow hb SYSTEMINCLUDEs for subsequently processed .pro files.
<?xml version="1.0"?>
<project name="run-qmake-${ant['sysdef.configuration']}" default="all">
<target name="all">
<if><available file="${r'$'}{build.drive}/epoc32/tools/qt/qmake.exe" type="file"/>
<then>
<sequential>
<#list data["//unit/@proFile/.."] as unit>
<#if (unit.@proFile=="hb.pro")>
<echo>Running configure.py for ${unit.@bldFile}/${unit.@proFile}</echo>
<if>
<available file="${r'$'}{build.drive}/${unit.@bldFile}" type="dir"/>
<then>
<exec executable="cmd" dir="${r'$'}{build.drive}/${unit.@bldFile}" failonerror="false">
<arg value="/C"/>
<arg value="python"/>
<arg line ="configure.py --qmake-bin=\epoc32\tools\qmake.bat --qmake-spec=symbian-sbsv2 --platform=symbian --qmake-options=MMP_RULES+=EXPORTUNFROZEN"/>
</exec>
</then>
<else>
<echo message="ERROR: Directory ${r'$'}{build.drive}/${unit.@bldFile} doesn't exist."/>
</else>
</if>
<echo>INFO: Exporting Orbit mkspecs to epoc32\tools for ${unit.@bldFile}/${unit.@proFile}</echo>
<copy file="${r'$'}{build.drive}/${unit.@bldFile}/hb_install.prf" todir="${r'$'}{build.drive}/epoc32/tools/qt/mkspecs/features" overwrite="true"/>
<copy file="${r'$'}{build.drive}/${unit.@bldFile}/hb.prf" todir="${r'$'}{build.drive}/epoc32/tools/qt/mkspecs/features" overwrite="true"/>
</#if>
</#list>
</sequential>
<parallel threadCount="${r'$'}{number.of.threads}">
<#list data["//unit/@proFile/.."] as unit>
<sequential>
<#if (unit.@proFile!="hb.pro")>
<echo>Running qmake for ${unit.@bldFile}/${unit.@proFile}</echo>
<if>
<available file="${r'$'}{build.drive}/${unit.@bldFile}" type="dir"/>
<then>
<exec executable="cmd" dir="${r'$'}{build.drive}/${unit.@bldFile}" failonerror="false">
<arg value="/C"/>
<arg value="qmake"/>
<!-- arg value="-listgen"/ -->
<#if unit.@qmakeArgs[0]??>
<arg line="${unit.@qmakeArgs?xml}"/>
<#else>
<arg line="${ant['qt.qmake.default.args']?xml}"/>
</#if>
<arg value="${unit.@proFile?xml}"/>
</exec>
</then>
<else>
<echo message="ERROR: Directory ${r'$'}{build.drive}/${unit.@bldFile} doesn't exist."/>
</else>
</if>
</#if>
</sequential>
</#list>
</parallel>
</then>
</if>
</target>
</project>