[Bug 244596] pkgbase: duplicate files and directories in `make packages`

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https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=244596

            Bug ID: 244596
           Summary: pkgbase: duplicate files and directories in `make
                    packages`
           Product: Base System
           Version: CURRENT
          Hardware: Any
                OS: Any
            Status: New
          Severity: Affects Only Me
          Priority: ---
         Component: misc
          Assignee: bugs at FreeBSD.org
          Reporter: emaste at freebsd.org

pkgbase `make packages` emits many duplicate file/directory warnings of the
form

pkg: duplicate directory listing: /boot/defaults, ignoring
pkg: duplicate file listing: /etc/libmap.conf, ignoring

In total,
485 duplicate directory
172 duplicate file

in some cases there are multiple lines in METALOG for a file or directory with
different attributes - e.g., ./etc has 80 copies of

./etc type=dir uname=root gname=wheel mode=0755 tags=package=utilities

and one

./etc type=dir uname=root gname=wheel mode=0755

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