Site hacked via undected google code?

See: https://code.google.com/p/wso-web-shell-2-8/ and http://killmalware.com/micmec.nl/
Blocked www.kace-undetected.com as Adguard malware…Rook Media abuse → https://www.virustotal.com/nl/ip-address/141.8.224.169/information/ Sality infested…
Re: http://toolbar.netcraft.com/site_report?url=http://micmec.nl
HTTP Server: Apache HTTP Server 2.4.10
Operating System: Unix
PHP Version: 5.4.31 (Outdated)
OpenSSL Version: 0.9.8e-fips-rhel5
Control Panel: cPanel
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polonus