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In the function php_cgi_ini_activate_user_config(), php_parse_user_ini_file() is never reached when path_len > doc_root_len
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My tests pass, maybe I oversaw something. Have to check again before final.
Can you test this patch http://pastebin.com/m183ef6ef? I did not test it yet but it looks like it could be the cause of this bug.
In any case I will test it and commit (or really fix it if this patch is not enough) later today.
Yes, that patch is effectively what I'm running at the moment and it works.
This bug has been fixed in CVS.
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Thank you for the report, and for helping us make PHP better.