extras: tools: add python 3.13 support for ninja

• Revert "extra: tools: use the ninja fork from Kitware"
• Update Ninja to 1.12.1
• Backport a patch from upstream ninja to add python 3.13 support

Starting from Python 3.13, Python does not support the configure script of the current version of the ninja we use. Hence update it to 1.12.1