CentOS

And if as pjsj2 inquired, it was compromised - there is NO coming back from that.

Thank you very much all. Your solutions worked out. yum reinstall \*.\*" and addressing the remaining permission mess with --setperms and setguids solved the issue. the files pjsr2 mentioned only still remaining and I ll investigate on that but system is back on track.
Thank you for the support specially lightman47 and pjsr2