System Workbench for STM32

I can't say why it works with Keil, but from what I can see, the fputc() function defines parameter as type FILE, whereas the struct declaration in the header is named __FILE (two leading underscores).

inputFunctionPointer and outputFunction pointers are members of the __FILE struct, but are _not_ members of FILE.

I would also advise that __FILE be declared as a type, like this:

typdef struct
{
...
}
__FILE;