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I had a call from a technician on a remote site with a Linux server (redhat ES 5.3) for which I assist with technical help.
What has happened for no apparent reason is that the entire /tmp directory was cleaned out (all files deleted) and file permissions of /tmp changed so that only root could write to it. Similar at the same time a number of sub directories in /var also disappeared.
To make things worse is that the affected machine won't let me make an ssh connection and GDM does not work either, so my only way to see what's going on is to ask the local technician to type command line commands and tell me the results over the phone. (the site is 1500 km away from me!)
What on earth could do something like that? I would consider it unlikely that the local technician could have done it, even unknowingly.
If local utilities have been replaced, or an obfuscation module added to the kernel, you MAY not be able to tell what is happening for certain even AFTER you recover access (if you even can).
Restoring ssh access is one start. If that fails, you might have him boot up and grant access using a live-cd image, then get ssh access, mount the drive, and do forensics from there. Running something like ROOTKITHUNTER may help you detect the cause of your issue IF it is malware triggered.