Re-generating the SoC/Software headers was causing some un-expected behaviours for users not familiar
with the flow. For example doing a --load with a different configuration, was re-generating the Software
headers and messing up things when trying to run software on the SoC.
Moving CRG simplify reset with NaxRiscv debug module and is in fact more logical.
Also do some minor updates/cosmetic changes while touching CRG/SoCCore.
Florent Kermarrec