Is there a way to encrypt or enclose my code on my Linux server after deployment? I know Zend does some kind of encryption, right? Is that what people use? Is this even poss
Do not trust the data coming from the browser - verify it and validate it.
Periodically do an audit of the processes on your machine and who can access them
Only have files in the document root that should be accessible by the outside world. Include files etc should not exist here
Check the log files periodically to check for suspect access.
For PHP errors/warnings - find a mechanism that does not give the client (browser) any info what has gone wrong. Send that to yourself. This is true for MySql as well.