For exec() and system(), we don't send any input and only capture stdout. So, everything except the stdout fileno can be closed-on-exec. The user can do the usual 2>&1 trick to get the stderr output as we run their command using the shell.
Unless I'm missing something, the post I sent illustrates an example where a file descriptor other than 0/1/2 is being used to communicate between the parent process and the child process. I don't think that close-on-exec on the fd's before exec() is any different than simply close()ing before we exec(), so I think that this five year old issue would surface if we go for that solution.
Back then, we couldn't come up with a good solution for this issue, and we simply disabled closing fd's on exec. We could alter this behavior to be optional, through php.ini, and yes, I don't particularly like this solution either, but I don't have any better in mind right now...
Zeev
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