Is there a way to run "native" commands from jsp?

Yes.  Something like this:

Process p = Runtime.getRuntime().exec("ls > ls.out");

I don't believe that will work.  Runtime.exec() is NOT a command line.  The following article explains why:

http://www.javaworld.com/javaworld/jw-12-2000/jw-1229-traps.html?page=4

(It's written in the context of Windows, but it applies to Linux as well.)

I went ahead and tried the piping command and, as predicted, it didn't work. I also tried Runtime.getRuntime().exec("/bin/sh -c 'echo Howdy | /usr/bin/mail -s testing me@mydomain.com'   >/dev/null 2>&1"); and that didn't work either; which was frankly surprising. Perhaps the stdout/stderr redirects messed it up. I removed those, but the return status was '2', and no message was sent. I may experiment further. I'll have to look up the '2' status.

However, putting it all in a shell script did work fine.

Right -- if you look at the article malfunction84 gave in a post above, you'll see the explanation.  You can't redirect stderr and stdout -- you have to handle them programmatically in your Java program.  So doing "/bin/sh -c 'xxxxx'" is fine, but >/dev/null is not.