Your server has been corrupted by Chaos. The Ordo Scharzenkommando recommends Exterminatus.

I'm totally serious though.
Do not boot the disk image. It's very easy for a skilled hacker to hide malware. No one is going to leave backdoor.py in your home directory.
Also, always make backups, daily if possible. Run a script every day to back up databases and put them in some database folder. Use rsync on a local computer to back up all the files and databases. Use a local backup system on your own computer that stores the versions of the files for each day so that you get a history of backups. Getting a daily backup of the server can be made really simple; it's very important to do. At least pay for Linode backups.
I'm planning to write about security advice here on the website for my GitHub profile:
http://inquisitor-sasha.sturmkrieg.ru/Here's the source for it if anyone wants to contribute; I can add push access
https://github.com/Inquisitor-Sasha/inq ... .github.ioAnd for backup advice and GitHub, upload any custom software that you use to GitHub so that you don't have to recreate it if you lose the linode. It will be open source, but unless you're actually planning to sell it, you might as well make it free for other people to use.
EDIT
Do not use PHPmyAdmin. It is a total backdoor.