I'm using suPHP with Apache 2 and users is allowed to use their own php.ini
How can I limit changes of global php.ini values to only few modications?
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Without knowing about any other in built method, I think your best bet would be to write a page that allows users to modify only the values you want them to. This way, not only can you control which settings they can change, but also limit the values to your own preferences. E.g. only allow upload_max_filesize to be between 16M and 25M.