math/polymake: Remove NATIVE option and add GitHub to MASTER_SITES

• Add GitHub as primary download site and upstream website as backup
• Remove NATIVE option, users wanting to apply CPU specific optimization

should use CPUTYPE instead using ports framework

• Use OPTIMIZED_CFLAGS option to define O3 optimization

PR: 273316
Reviewed by: Philipp Ost <bsd@philippost.de> (maintainer)
Sponsored by: Blinkinblox