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

How to run source *.sh before build at SW4STM32

“Import > General > Existing Projects into Workspace” imports a project without modifying the settings. The Makefile is automatically generated when building the project (pre-build and post-build are added to the generated makefile)

“Import > C/C++ > Existing Code as Makefile Project” creates a new Eclipse generic makefile project (and not System Workbench project). It means that you provide your own Makefile so you can modify it.
By the way, If you really wanted to import a Makefile project, my advise to create a new project then copy/paste your sources into it.
New > C Project, select Makefile project and Ac6 STM32 MCU GCC toolchain.