OK:
FatFS and USB_Device_Library are provided by third parties, and are considered middleware. So somewhere in the project configuration you have FatFS selected and also USB support. They never come in for my projects unless I have selected those options in the IOC file.
Now, for the system_sem32f4xx.c file:
I don't know why it's there, either. It causes multiple definitions.
However, deleting it is not the answer. The next time you make any changes that cause the system to regenerate code from the IOC file, THAT FILE will be put back, and you will just have to delete it again.
GIve it a try and see if it happens. Change something trial, like the baudrate on a serial port that you can easily change back. Bet the file magically appears. Been there, done that.
The solution (or at least the workaround) is to highlight that unwanted file. Right click and select properties. On the second screen of properties, you should see an option "remove from build". Check that.
That tells the compiler to NOT build the file, just as if you'd put an #ifdef that is not satisfied around the source code. BTW: THAT does not work since the file is completely regenerated and will likely remove the #ifdef unless you find a "user code" section.
Since the IOC builder does NOT change the file properties, once ignored, the file will stay ignored. Let the IOC builder do what it wants.
STMicro cannot duplicate this problem, I've reported it every few years or so.
