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

Confused about directory structure with STM32CUBEMX plugin and Eclipse

I’ve found a very simple (and more comfortable) solution to get around this problem:

Create 2 symbolic links in your filesystem in smt-test/SW4STM/smt-test:

1.: link to ../../Src
2: link to ../..Inc

Next in Eclipse exclude smt-test/Application/User from build.

From now on, you can create your source and headers as usual in Src and inc, and everybody is happy (including CubeMX)