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

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

--- Comment #5 from Ed Maste <emaste@freebsd.org> ---
There was a bug in the way the inode lookup was done, see
https://reviews.freebsd.org/D37412 for the fix.

With that fixed when testing against recent main I get:

% tools/pkgbase/metalog_reader.lua -c <path>/amd64.amd64/stage/METALOG | grep
'same inode'

error: entries point to the same inode but have different meta:
./etc/pam.d/ftpd,./etc/pam.d/ftp in line 1997,1998. off by "mode"
error: entries point to the same inode but have different meta:
./usr/libexec/dwatch/io-start,./usr/libexec/dwatch/io-done,./usr/libexec/dwatch/io
in line 13138,13137,13118. off by "mode"
error: entries point to the same inode but have different meta:
./usr/libexec/dwatch/vop_mknod,./usr/libexec/dwatch/vop_mkdir,./usr/libexec/dwatch/vop_create,./usr/libexec/dwatch/vop_remove,./usr/libexec/dwatch/vop_rmdir,./usr/libexec/dwatch/vop_lookup
in line 13198,13197,13131,13199,13200,13196. off by "mode"
error: entries point to the same inode but have different meta:
./usr/libexec/dwatch/recvfrom,./usr/libexec/dwatch/recvmsg,./usr/libexec/dwatch/sendto,./usr/libexec/dwatch/send,./usr/libexec/dwatch/sendrecv,./usr/libexec/dwatch/sendmsg,./usr/libexec/dwatch/recv
in line 13172,13173,13176,13174,13126,13175,13171. off by "mode"
error: entries point to the same inode but have different meta:
./usr/libexec/dwatch/udplite,./usr/libexec/dwatch/udplite-receive,./usr/libexec/dwatch/udplite-send
in line 13130,13194,13195. off by "mode"
error: entries point to the same inode but have different meta:
./usr/libexec/dwatch/chmod,./usr/libexec/dwatch/fchmodat,./usr/libexec/dwatch/lchmod
in line 13116,13135,13136. off by "mode"
error: entries point to the same inode but have different meta:
./usr/libexec/dwatch/open,./usr/libexec/dwatch/openat in line 13122,13141. off
by "mode"
error: entries point to the same inode but have different meta:
./usr/libexec/dwatch/tcp-io,./usr/libexec/dwatch/tcp-accept,./usr/libexec/dwatch/tcp-connect-established,./usr/libexec/dwatch/tcp-established,./usr/libexec/dwatch/tcp-receive,./usr/libexec/dwatch/tcp-connect,./usr/libexec/dwatch/tcp,./usr/libexec/dwatch/tcp-init,./usr/libexec/dwatch/tcp-state-change,./usr/libexec/dwatch/tcp-connect-request,./usr/libexec/dwatch/tcp-accept-established,./usr/libexec/dwatch/tcp-status,./usr/libexec/dwatch/tcp-accept-refused,./usr/libexec/dwatch/tcp-refused,./usr/libexec/dwatch/tcp-connect-refused,./usr/libexec/dwatch/tcp-send
in line
13186,13177,13181,13184,13187,13180,13128,13185,13190,13183,13178,13191,13179,13188,13182,13189.
off by "mode"
error: entries point to the same inode but have different meta:
./usr/libexec/dwatch/udp,./usr/libexec/dwatch/udp-send,./usr/libexec/dwatch/udp-receive
in line 13129,13193,13192. off by "mode"
error: entries point to the same inode but have different meta:
./usr/libexec/dwatch/write,./usr/libexec/dwatch/rw,./usr/libexec/dwatch/read in
line 13153,13124,13152. off by "mode"
error: entries point to the same inode but have different meta:
./usr/libexec/dwatch/ip-receive,./usr/libexec/dwatch/ip,./usr/libexec/dwatch/ip-send
in line 13139,13119,13140. off by "mode"
error: entries point to the same inode but have different meta:
./usr/libexec/dwatch/sched-surrender,./usr/libexec/dwatch/sched-queue,./usr/libexec/dwatch/sched-sleep,./usr/libexec/dwatch/sched-change-pri,./usr/libexec/dwatch/sched-off-cpu,./usr/libexec/dwatch/sched-on-cpu,./usr/libexec/dwatch/sched-pri,./usr/libexec/dwatch/sched-enqueue,./usr/libexec/dwatch/sched-tick,./usr/libexec/dwatch/sched-load-change,./usr/libexec/dwatch/sched-wakeup,./usr/libexec/dwatch/sched-cpu,./usr/libexec/dwatch/sched-lend-pri,./usr/libexec/dwatch/sched-dequeue,./usr/libexec/dwatch/sched,./usr/libexec/dwatch/sched-exec,./usr/libexec/dwatch/sched-preempt,./usr/libexec/dwatch/sched-remain-cpu
in line
13168,13165,13167,13154,13161,13162,13164,13157,13169,13160,13170,13155,13159,13156,13125,13158,13163,13166.
off by "mode"
error: entries point to the same inode but have different meta:
./usr/libexec/dwatch/proc,./usr/libexec/dwatch/proc-exec-success,./usr/libexec/dwatch/proc-signal,./usr/libexec/dwatch/proc-signal-discard,./usr/libexec/dwatch/proc-create,./usr/libexec/dwatch/proc-signal-clear,./usr/libexec/dwatch/proc-signal-send,./usr/libexec/dwatch/proc-exec,./usr/libexec/dwatch/proc-status,./usr/libexec/dwatch/proc-exec-failure,./usr/libexec/dwatch/proc-exit
in line 13123,13145,13147,13149,13142,13148,13150,13143,13151,13144,13146. off
by "mode"
error: entries point to the same inode but have different meta:
./.profile,./root/.profile in line 2203,2202. off by "mode"
error: entries point to the same inode but have different meta:
./root/.cshrc,./.cshrc in line 2209,2211. off by "mode"

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