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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Using Git

i use git with CubeMX project in eclipse w/o any problem , external tool are not necessarly required ( maybe just simpler).
how to do it all in eclpise
have your project Generated by CubeMX (do not use option to link all file but instead copy all or only require file to project)
in eclipse create a new project with new -> project - (generic project )
in the dilaog
untick “default location”
give the project a name
then browse to the CubeMX top tree folder
et git it
Now project-> team ->Share

to keep git repo on the same place/ folder tick “use or create repository in praent folder of project ”
in dialog bottom use “create”

voila ... all done , commit everyhing straigh away (select all files)
Now you can import the ac6 proejct from the source tree in git repo view (import existing prioject)
if gire repo view is not visible “window ->show view ->other -> git -> repo ...”

Take care eclispe easily mess up if you open the same file mutliple time (ie the one from the top project and the same linked from ac6 project).
to avoid that simply close or delete( just from explorer view do not delete from file system) top project

note thay under window Mysgit or some mingw-msys package ( https://sourceforge.net/projects/mingwbuilds/files/external-binary-packages/)Question provide git/svn/... command line .

if you want to keep include form an example cube (not cubemx) project it is not so easy/possible as all project link files to the same local library source , so it woudl require to version everything to get include (and all drivers midleware etc source as well) :-(