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Pretty much all git repos on o3 broke over night:

fatal: .git/index: index file smaller than expected

was printed for /var/lib/openqa/tests/{opensuse,openqa,obs}/ as well as /var/lib/openqa/tests/opensuse/products/opensuse/needles`.

The .git/index file had 0 size for them.

The index file of the needles repo had a birthtime of 2021-10-09 22:41:05.923862229 +0000, which conincides with a cron run of fetchneedles:

From geekotest@ariel.suse-dmz.opensuse.org  Sat Oct  9 22:41:09 2021
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From: "(Cron Daemon)" <geekotest@ariel.suse-dmz.opensuse.org>
To: geekotest@ariel.suse-dmz.opensuse.org
Subject: Cron <geekotest@ariel>     env updateall=1 force=1 /usr/share/openqa/script/fetchneedles
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X-Cron-Env: <XDG_SESSION_CLASS=background>
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X-Cron-Env: <LC_CTYPE=en_US.UTF-8>
X-Cron-Env: <SHELL=/bin/sh>
X-Cron-Env: <HOME=/var/lib/openqa>
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Date: Sat,  9 Oct 2021 22:41:04 +0000 (UTC)

fatal: It seems that there is already a rebase-merge directory, and
I wonder if you are in the middle of another rebase.  If that is the
case, please try
        git rebase (--continue | --abort | --skip)
If that is not the case, please
        rm -fr ".git/rebase-merge"
and run me again.  I am stopping in case you still have something
valuable there.

Use force=1 to discard uncommitted changes before rebasing

From geekotest@ariel.suse-dmz.opensuse.org  Sun Oct 10 08:31:04 2021
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From: "(Cron Daemon)" <geekotest@ariel.suse-dmz.opensuse.org>
To: geekotest@ariel.suse-dmz.opensuse.org
Subject: Cron <geekotest@ariel>     env updateall=1 force=1 /usr/share/openqa/script/fetchneedles
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X-Cron-Env: <XDG_SESSION_TYPE=unspecified>
X-Cron-Env: <XDG_SESSION_CLASS=background>
X-Cron-Env: <LANG=en_US.UTF-8>
X-Cron-Env: <LC_CTYPE=en_US.UTF-8>
X-Cron-Env: <SHELL=/bin/sh>
X-Cron-Env: <HOME=/var/lib/openqa>
X-Cron-Env: <PATH=/usr/bin:/bin>
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Message-Id: <20211010083104.D457D18B5F@ariel.suse-dmz.opensuse.org>
Date: Sun, 10 Oct 2021 08:31:04 +0000 (UTC)

fatal: .git/index: index file smaller than expected
fatal: .git/index: index file smaller than expected
fatal: .git/index: index file smaller than expected
Use force=1 to discard uncommitted changes before rebasing
fatal: .git/index: index file smaller than expected
fatal: .git/index: index file smaller than expected
fatal: It seems that there is already a rebase-merge directory, and
I wonder if you are in the middle of another rebase.  If that is the
case, please try
        git rebase (--continue | --abort | --skip)
If that is not the case, please
        rm -fr ".git/rebase-merge"
and run me again.  I am stopping in case you still have something
valuable there.

Use force=1 to discard uncommitted changes before rebasing
fatal: .git/index: index file smaller than expected
fatal: .git/index: index file smaller than expected
fatal: .git/index: index file smaller than expected
Use force=1 to discard uncommitted changes before rebasing

I fixed those repos manually by doing git reset --quiet; git status; git pull.
The openqa tests repo needed a manual rebase to deal with a conflict.

The fatal: It seems that there is already a rebase-merge directory error is probably a red herring, because it is only printed once while multiple repos are broken, it's still printed after the index purge and has been going on since Wed, 14 Jul 2021 17:30:10 +0000 (UTC) according to root's mailbox.

All of the error logs ended up in /var/spool/mail/root, which probably should be archived:

ariel:~ # ll -h /var/spool/mail/root
-rw------- 1 root root 508M Oct 11 08:32 /var/spool/mail/root
ariel:~ # wc -l /var/spool/mail/root
10018188 /var/spool/mail/root