Hi Ashley,

I guess this change is the cause: https://reviews.freebsd.org/D20173
It marks the group and the master.passwd file for inclusion in the 
FreebSD-runtime package.
I tried this change on my 12 system, the files are included in the
package. You also see them in the runtime.plist file, but as regular file,
not marked as a config file, like the motd file for example.
 
...
@(root,wheel,0644,) /etc/group
@(root,wheel,0600,) /etc/master.passwd
@config(root,wheel,0644,) /etc/motd
...
 
i guess now the existing file is replaced by the new file, instead of beeing
merged with it.
i think, the tag "config" must be added to the above patch. But i am not sure,
what the sytnax looks like for this.
 
--
Martin
 
> After building and installing -CURRENT r347469 using in-tree pkgbase, I
> discovered that my /etc/group, /etc/passwd, /etc/master.passwd,
> /etc/pwd.db and /etc/spwd.db had been overwritten.
> 
> I encountered this after running 'make packages', installing into a
> ZFS Boot Environment using bectl to create and mount a new BE, running
> 'pkg -r $mounpoint upgrade -y' and 'pkg -r $mountpoint -yg "FreeBSD-*"'
> to upgrade the packages and insure that new base packages got installed,
> and finally unmounting and activating the BE.
> 
> ~Ashley Chase
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