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Yes, then it would be better to have all the software vendors out there who 'require' Ioncube to change the way to implement their wares?
That's exactly right.
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Trouble is that a lot of applications, CMS's and other tools are suggesting they 'require' Ioncube.
No software 'requires' ioncube. The coder made a judgement call to obfuscate data. Usually this is done to obscure methodology (for whatever reason). Some scripts use it to protect copywritten content, others use it to hide the fact they've ripped off other's code, and the worst hide their evilness inside the encrypted bits.
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Trouble is that a lot of applications...are elegant and user friendly...
They're the ones that don't "require" ioncube, fopen, register globals, etc.
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1. Having already installed custom PHP as per this instruction:
http://wiki.dreamhost.com/Installing_PHP5 (to the letter)
There are multiple solutions on the page you linked, which one did you attempt?
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we now have a info.php (btw phpinfo.php will not work for some reason on my domain...)
Notepad them. What's the difference between the info.php and phpinfo.php you allude to?
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If the loaded configuration file is here...
Perhaps PHP is being directed to an incorrect location.
I couldn't make a call on that without clearer information.
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Does this whole exercise require a server reboot (as per instructions)
No reboot is required as DH uses the better approach. (See ioncube site re: runtime).
To which instructions regarding a reboot are you referring?
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... how can we start from scratch and make sure we get this right?
*Very Carefully* delete all files the installation(s) created within root and domain.com, including directories, with the command rm -rf dirname. You can ascertain the directories & files created by reading the script(s) you used. Most scripts appear to rely on an etc folder, so be sure there aren't any files in there that *don't* pertain to your customised PHP before removing it from root. You wouldn't want to inadvertently break something else whilst endeavouring to fix this (something I've learned the hard way - a few times lol).