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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 (registration required) various documents highlighting:

System Workbench for STM32


How to reset target MCU during debugging

I also find this a great pain. It has been on the todo list close to a year now. Maybe you would like to try out CoIDE. It has Mcu reset button. Also, you can disable the programming of the binary image to the mcu on the initiation of debugger and programming it at will with a single click of button later.