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I'm not a PHP coder and don't particularly do any heavy web programming, however to understand the broad aspects of web security I'd suggest learning not only PHP but others too. If you want to code in PHP then yeah learn php from cover to cover however in web app security you may be better having a general knowledge of numerous languages. Just my opinon, unfortunately php is one of the few languages I don't have ebooks for lol... possibly not very helpful sorry.
W3Schools is best for that sort of stuff.