Posted on May 04, 2016 at 09:03AC6 has very little to do with the HAL and nothing to do with Cube. They provide the BSP and put it on top of ST's HAL when you create your project from within Eclipse.
If you use Cube to create your project, you bypass the inclusion of the BSP.
From teaching my class and playing with AC6, I have found the BSP to be, initially, convenient, but generally not necessary. Then when you look at some of the code, like for the gyro on the 401C discovery board, WOW such bad code. Needless object oriented misguidedness for something that gets instantiated exactly once, and debugged by everybody.
I suggest that you take the good bits from the BSP that you like and create your own. I never found LED3 to be very useful. Put in some good names in Cube and use the defines in mxconstants.h. I layered on LED_BLUE over the BSP LED3 (or whatever it was) almost immediately.
I find that Cube is much more useful for bringing up a board and getting me to the point where I can lay on my application code.
Andrei from The Great White North
(as seen on the Embedded.fm podcast and the Embedded Wednesdays posts on Embedded.fm/blog)
