In the C library, the setting up of the group array by various
utilities is done by calling gr_addgid() for each group to be
added (usually found by traversing /etc/group) then calling the
setgroups() system call after the group set has been created.
The gr_addgid() function (helpfully?) deduplicates the addition
of group members. So, if you call it to add a group member that
already exists, it is just dropped. Because group[0] is the
effective group-ID and is over-written when a setgid program
is run, The value in group[0] is usually duplicated so that
group value is not lost when a setgid program is run.

Historically this happened because the group value indicated
in the password file also appears in /etc/group (e.g., if you
are group staff in the password file, you will also appear in
the staff line in /etc/group). But, with the addition of the
deduplication, the attempt to add group staff was lost because
it already appeared in group[0]. So, the fix is to deduplicate
starting from group[1] which allows a duplicate of the entry in
group[0], but not in later entries.

There is some confusion about the setgroups system call because in
BSD it has (always) set the entire group including the egid group
(in group[0]). However, in Linux, it skips over group[0] and starts
setting from group[1]. See this comment from linux_setgroups:

/*
 * cr_groups[0] holds egid. Setting the whole set from
 * the supplied set will cause egid to be changed too.
 * Keep cr_groups[0] unchanged to prevent that.
 */

To make it clear what the BSD setgroups system call does, I
added the following paragraph to the setgroups(2) manual page:

The first entry of the group array (gidset[0]) is used as the effective
group-ID for the process.  This entry is over-written when a setgid
program is run.  To avoid losing access to the privileges of the
gidset[0] entry, it should be duplicated later in the group array.
By convention, this happens because the group value indicated in the
password file also appears in /etc/group.  The group value in the
password file is placed in gidset[0] and that value then gets added a
second time when the /etc/group file is scanned to create the group set.

Reported by: Paul McMath paulm at tetrardus.net
Reviewed by: kib
MFC after: 2 weeks