pkgbase: examine METALOG files relative to stage root directory

Previously we stripped the '.' from the beginning of each METALOG entry
to determine the path to stat. This meant that we examined files on the
build host, not the staged files.

Instead, strip off the last part of the specified METALOG pathname to
find the stage root directory, and stat files relative to that.

Reviewed by: bapt
Sponsored by: The FreeBSD Foundation
Differential Revision: https://reviews.freebsd.org/D37412