makeroot.sh: allow duplicate entries even with -f <filelist>

makefs disallows duplicate entries unless the -D option is specified.

Previously makeroot.sh enabled -D unless a filelist was provided via
the -f options. The filelist logic creates an mtree manifest from the
METALOG and the provided filelist by passing them through sort -u,
so duplicates were not expected. However, duplicates can still occur
when a directory appears in multiple packages -- for example,

./etc/pam.d type=dir uname=root gname=wheel mode=0755
./etc/pam.d type=dir mode=0755 tags=package=runtime
./etc/pam.d type=dir mode=0755 tags=package=at
./etc/pam.d type=dir mode=0755 tags=package=ftp
./etc/pam.d type=dir mode=0755 tags=package=telnet

For the purposes of makefs these directory entries are identical, but
are of course not identical for sort -u.

For now just leave the allow duplicates -D flag enabled.

PR: 228606
Sponsored by: The FreeBSD Foundation