<snip>
2) user cannot trick other root processes to read
script.php for her.

Is there a better alternative?
</snip>

Depending on your budget yes there is.  Zend has a PHP encoding utility
which performs two functions, first off since it needs to run through their
optimizer your PHP scripts will tend to run faster (at the expense of a bit
more memory consumption) and also you don't need to worry about preventing
the source code from being read as the php scripts are converted into a
binary executable.  License to use these programs are I believe around $600
per year but offer a wide range of additional features but I would consider
it well worth it to a company rather than spending countless tech hours and
security testing to prevent the source from being viewed.

http://www.zend.com

Sincerely,

Craig Vincent


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