BTW. @sheepdoll posted onto another F4 thread about the Cube, and from what I understand, there may be licensing issues on the linker scripts it generates.
Though @sheepdoll may have been also referring to OpenSTM32 workbench , and I'm not sure where it gets its files.
The restrictive license on the STM32F401RETx_FLASH.ld file must come from the STM32CubeMX. The same file with a different copyright/license header is created when TRUESTUDIO is chosen as the IDE. Other than the copyright the files are identical. So I think this is boilerplate code for use with GCC tools through eclipse. As for where the files come from, there seem to be some databases in the users home directory, in a folder called .stm32cubemx.
I was not impressed with Koduino. Seems to have a lot of the same issues the AreoQuad stuff has regarding what chip targets are used. The F401 and the F407 are not the same, then there are the Nucleo and Discovery differences. It could just be that I have been working with the tools here and am feeling more comfortable with them.