Move ports management to git

Update FreeBSD ports management scripts to support git and automatically convert non-git ports trees
auto-update-pkgsrc: New script to update pkgsrc tree and installed packages via pkgin, pkg_chk, or pkg-rolling-replace
auto-update-system: Factor out auto-update-pkgsrc and add base updates for MacOS using softwareupdate
Add pkgsrc support to auto-mark-install-from-source and auto-mark-pkg-critical
A few other minor bug fixes and enhancements