SW4STM32 and SW4Linux fully supports the STM32MP1 asymmetric multicore Cortex/A7+M4 MPUs

   With System Workbench for Linux, Embedded Linux on the STM32MP1 family of MPUs from ST was never as simple to build and maintain, even for newcomers in the Linux world.
And, if you install System Workbench for Linux in System Workbench for STM32 you can seamlessly develop and debug asymmetric applications running partly on Linux, partly on the Cortex-M4.
You can get more information from the ac6-tools website and download two short videos (registration required) highlighting:

System Workbench for STM32

Create script failure: fail to retrieve target

I also have a similar problem, generated project through CubeMX but unable to flash or debug. For me it worked editing the .cproject file.
All i needed to do was to change any entries of fr.ac6.managedbuild.option.gnu.cross.board, from 32F769IDISCOVERY to STM32F769I-DISCO.
Of course you have to modify yours accordingly.

Hope this might help someone as I really lost quite long time finding what the issue was.