System Workbench for STM32

"I still had to use a "../../" relative addressing strucutre equal to the on-disk folder/file structure"

Did you try to add the include paths to your build settings? I'm doing this with success everytime I add any new hearder file to the project. The indexer does this for you, and you don't need to provide full path where the file resides.

Regarding CubeMx, I never had luck compiling any piece of code it has generated. I found it much easier and less error-prone to manuall add the libraries you want in the IDE. However, even the newest HAL doesn't work in harmony with AC6 out of the box. Go and create a new C Project, use the HAL Firmward for STM32F429, add the FreeRTOS, Fat, and STemWin components to your project, compile with ARM-none-eabi, and let me know if that worked right away!

I spent two days, too, trying to figure out the linking issue for the STemWin pre-compiled library in AC6. Still the linker complains about certain issues.

I will try to open another thread for the STemWin, hopefully I would get an advice!

Cheers!