FreeBSD: migrate to newer pkg_create(3) API
The pkg_create_from_manifest() function was never really intended as stable API, and bapt@ has asked me to stop using it so the public API can be stabilized.
Port to pkg_create() with its attendant settings struct. Since we already have a complete manifest file, we can hand that (including the embedded plist) to pkg_create().
While here, reintroduce pkg_init(), which lived in downstream patches for a while and then went away again.