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Just been looking through some servers and seen that the external ip is set up with the full and short names the wrong way round, e.g.:

a.b.c.d myserver myserver.mycompany.org

What sort of problems can this cause, given that nsswitch.conf is configured with files as the primary hostname resolver?

At present it doesn't seem to be causing us any direct problems for us (besides hostname/hostname -f returning the short name), but I need to know how urgent it is that we fix this.

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If it isn't broke don't fix it.

To coin a phrase, often with web application deploys you may find that the FQDN is in /etc/hosts for loop back purposes (cron jobs and the like).

In your case if your FQDN is pointing to the real world IP it could be it has been placed there to prevent the need for DNS look ups of the external domain, again this could be due to some internal process.

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