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

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Problems with System Workbench

I’m not sure what function you’re using to flash the board, but if you use the Run (Ctrl-F11) command from the Run menu, it will flash your latest build of the firmware onto your target, then reset and run it. I think this is the function you’re looking for.

I don’t recall if Run -> Run requires a pre-existing “Run configuration” to be created or not. You may be prompted to set one up the first time you attempt to run your application this way. You should be able to use default settings with the “AC6 STM32 Debugging” template if you are prompted to create one.