In php.ini file:
 auto_append_file =/usr/local/apache/htdocs/www/after.phtml

File test.phtml:
<?
 test();
?>

File after.phtml:
<?
 echo "after.phtml start<br>";
 function test()
   {
    echo "test";
   }
 echo "after.phtml end<br>";
?>

When I run file test.phtml I see the message:

"Fatal error: Call to undefined function: test() in /usr/local/apache3/htdocs/www/oc/test.phtml on line 2"

After removing the call of test() function in test.phtml everything works OK. It shows:

after.phtml start
after.phtml end