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RTFM

I am confused...

Documentation says:

With safe mode enabled, all words following the initial command string are treated as a single argument. Thus, echo y | echo x becomes echo "y | echo x".

Try this with safe_mode enabled:

file args.sh
#!/bin/sh

echo First arg: $1
echo Second arg: $2

and php:
passthru('args.sh one two');

According to doc, I shoud get:
First arg: one two
Second arg: 

But I get:
First arg: one
Second arg: two


So echo y | echo x doesn't become echo "y | echo x" but echo y \| echo x.