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    <p>What you describe is normal.</p> <p>You have PHP files that are reachable in your www directory so apache (or your favored webserver) can read and process them. If you move them out you can't reach them anymore so there is no real option of that sort.</p> <p>After all your PHP files for AJAX are just regular php files, likely your other project also contains php files. Right ? They are not more or less at risk than any script on your server.</p> <p>Make sure you program "clean". Think about evil requests when writing your php functions, not after writing them. As you already did: correctly quote all incoming input that might hit a database or sensitive function.</p> <p>You can add security checks on your incoming values and create an automated email if you detect someone trying evil stuff. So you'll likely receive a warning in such cases. But on the downside: You'll regularly receive warnings because some companies automatically scan websites for possible bugs. So you will receive a warning on such scans as well.</p> <p>On top of writing your code as "secure" as you can, you may want to add a referer check in your code. That means your PHP file will only react if your website was given as referer when accessing it. That's enough to block 80% of the kids out there. But on the downside: a few internet users do not send a referer at all, some proxies filter that. (I personally would ignore them, half the (www) internet breaks on them anyway)</p> <p>One more layer of protection can be added by htaccess, you can do most within PHP but it might still be of interest for you: <a href="http://httpd.apache.org/docs/2.0/howto/htaccess.html" rel="nofollow">http://httpd.apache.org/docs/2.0/howto/htaccess.html</a></p>
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