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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 add files to an MX generated project

I still struggle with some of this myself but,
possibly I can offer some thoughts.

I have been twiddling with the STM32CubeMX and System Workbench, and I find that the STM32CubeMX structure is good for me.

It putes the BSP in the Application/User folder where one also finds main.

Most of the files listed in the project appear to be in virtual directories, that is, I see them in Eclipse in one way and if I look on the disk drive, they are in different places.

I found that you must use the import to bring in more .c files and also .h files, after some experiemnting with the import and multiple failed attmpts, I seem to be able to duplicate my efforts with some twiddling.

Once you get used to Eclipse, the rest should fall into place.