FreeRTOS running, SUCCESS!
I suspect that ongoing development of STM32CubeMX and System Workbench will improve the integration of each and thier interoperability.
As to adding either .c or .h files to a project, in the cae of .c files, you select the virtual folder in the project tree and use the Import menu and choose the file from the File System. When adding .h files, I found that putting them where I want them first in the file system and then using the Import menu to choose the file and import it works.
I imported the BSP package for the STM32F4 Discovery, first copying the ST folder to the Drivers folder that corresponded to the Drivers in the Projetc Tree. Then I Imported the folder from the File System, only choosing specific folders to Import. I ended up deleting some stuff from the Projetc Treee after and even though it was still on the disk, Eclipse ignored it in the build.
I have to admit, a Shared Library is a much better way to go, I see an option in Stm32CubeMX to leave all the files behind in the repositry, I wonder if that is STMs attempt at a Shared Library?