You're executing three commands in a row. Each command should be a separate Process. Also, the command and the parameters should be broken out into elements of the array:
Process send1 = Runtime.getRuntime().exec(new String[] {"javac", "/tmp/"+ fileName});
send1.waitFor(); // this returns an int with the exit status of the command - you really should check this!
Process send2 = Runtime.getRuntime().exec(new String[] {"sed", "-i", "s/Foo/Foo2/g", "/tmp/"+ fileName});
send2.waitFor();
Process send3 = Runtime.getRuntime().exec(new String[] {"java", "/tmp/"+ fileNameShort+".class"});
send3.waitFor();
Alternately, feed the whole thing to sh -c (though you really, really should use the previous method as then you don't have to worry about escaping arguments etc.)
Process send = Runtime.getRuntime().exec(new String[] {"sh", "-c", "javac /tmp/"+ fileName + "; sed -i 's/Foo/Foo2/g' /tmp/"+ fileName + "; java /tmp/"+ fileNameShort + ".class"});