I'm also looking at the generic_clock.c file (I didn't change it before, so was running at the default) but I have a question:

On the wiki, it states use the HSI for the PLL Mux, however doing this in CubeMX, it tells me PLL Source Mux must use HSE as input - what do I do here?

This is the clock config so far :

It is an advice when you configure the USB. HSE is more stable.

Okay, so I've tried that, and the code that it generates doesn't work - the processor doesn't appear to run

If I disable the USB, the generated clock init code works fine. I'll look at creating the usb clock init manually, instead of using cubeMX

Hi @jamesrlucas
Thanks for the update.
I don't see any issue in your clock config and don't know why it does not work.
Maybe using HSI with USB enabled leads to an issue.

I've updated your branch: squash all commit and apply astyle so think to fetch it before doing any other modifications.

I've found the issue with the clock - CubeMX is missing the RCC Oscillator initialization steps if I generate the code with the internal oscillator as the USB source (as per the screenshot above) - Clearly it doesn't like the USB + HSI option...

Disabling the USB interface in CubeMX generates a working clock config, I'm using this currently for my project.
Enabling the external oscillator also generates what looks to be a working clock config, but I haven't tested this yet.

Will test this further and commit a clock config when I get chance.