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Keil IDE with MXCube mismatched projects

Folks,
is it just me or other come across this problem.
Using the Latest version of both tools.

Starting a new project with the Hardware engineers giving me a STM mxCube project
to get started on.

Starting one with Keil, I select the right micro, from the runtime options select CMSIS RTOS02 API
using libraries and the Device STM32 Cube Framework (API) clicking on the STM32CubeMx option

After clicking on OK at the bottom of the Dialog box it launches MxCube

This is a blank Cube project only getting the micro correct.
So importing the Hardware engineer mxCube Project into MxCube

There is first a conflict with the micro clock source and settings.

So correct that, then get mxCube to generate the source code for the hardware etc you are presented
with an option to open project.

Well now the Keil runtime options are lost. and there is a whole new file structure below the Device folder
that has a code from the Cube etc and RTE in

adding in the runtime options back in there are conflicts with device startup code eg both tools have generated it and included it in the Keil project

Doing it the other way eg mxCube first generate the Keil project then add in the Keil runtime options I run into similar conflicts about startup but
I have to exit the Keil IDE because now headers like cmsis_os2.h is having problems with typdefs

its a mess

So anyone have a seamless project start using Keil and ST mxCube ?