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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


.project file links duplicted during STM32CubeMX code regeneration

I was contractor on this project for several months, and have since moved on. I’m working from memory here so your results may vary and this may not be completely how I did it but hopefully you’ll get the idea.

Source control is essential, be sure you have a committed version before you perform the changes in CubeMX.
AFter changes in CubeMX, compare in the .project file against the committed version, and look at the file link difference. (we were using subversion, diff with winmerge or meld). Some manual comparing and editing is required. Forunately the order of the files is normally kept in tact so the compare is not terrible.
In your difference viewer, in the new file, delete the section of old file paths that match committed version and refresh. The new diff will show the old file paths nearly matching the file paths with the bad locationURI, plus and additons and deletions, from here you should be able to update the old paths from the committed version (keep in mind additions and deletions).

You may also try to re-arrange the order of the files before editing in CubeMX.. I also did find in some cases re-creating the project resulted in a different file order in the .project file, and the edits from CubeMX worked correctly.

Good luck.