Perhaps Jay has a point, but I don't think so. To confirm this, you can probably check some variable in phpinfo, or you can run 'whoami'.
How are you running ls -ld? system? exec? Try backticks or shell_exec().
Tried popen() and backticks. I do not think that the other functions would change anything. `whoami` executed under php returns "apache", as we suspected.
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