Update run-qmake template to run Orbit configure.py first, followed by mkspec export. This should allow hb SYSTEMINCLUDEs for subsequently processed .pro files.
@echo off
setlocal
if not defined HELIUM_HOME set HELIUM_HOME=%~dp0..\..\..\..\helium
echo %HELIUM_HOME%
rem call ..\..\build\env.bat
call %HELIUM_HOME%\hlm.bat %*
endlocal