感谢Greg和Dave的反馈。并不是我想要的，但是我决定花一些时间研究它，并提出了一个快速而肮脏的解决方案：

<?php
    $functions = array();
    $path = "/path/to/my/php/project";
    define_dir($path, $functions);
    reference_dir($path, $functions);
    echo
        "<table>" .
            "<tr>" .
                "<th>Name</th>" .
                "<th>Defined</th>" .
                "<th>Referenced</th>" .
            "</tr>";
    foreach ($functions as $name => $value) {
        echo
            "<tr>" . 
                "<td>" . htmlentities($name) . "</td>" .
                "<td>" . (isset($value[0]) ? count($value[0]) : "-") . "</td>" .
                "<td>" . (isset($value[1]) ? count($value[1]) : "-") . "</td>" .
            "</tr>";
    }
    echo "</table>";
    function define_dir($path, &$functions) {
        if ($dir = opendir($path)) {
            while (($file = readdir($dir)) !== false) {
                if (substr($file, 0, 1) == ".") continue;
                if (is_dir($path . "/" . $file)) {
                    define_dir($path . "/" . $file, $functions);
                } else {
                    if (substr($file, - 4, 4) != ".php") continue;
                    define_file($path . "/" . $file, $functions);
                }
            }
        }       
    }
    function define_file($path, &$functions) {
        $tokens = token_get_all(file_get_contents($path));
        for ($i = 0; $i < count($tokens); $i++) {
            $token = $tokens[$i];
            if (is_array($token)) {
                if ($token[0] != T_FUNCTION) continue;
                $i++;
                $token = $tokens[$i];
                if ($token[0] != T_WHITESPACE) die("T_WHITESPACE");
                $i++;
                $token = $tokens[$i];
                if ($token[0] != T_STRING) die("T_STRING");
                $functions[$token[1]][0][] = array($path, $token[2]);
            }
        }
    }
    function reference_dir($path, &$functions) {
        if ($dir = opendir($path)) {
            while (($file = readdir($dir)) !== false) {
                if (substr($file, 0, 1) == ".") continue;
                if (is_dir($path . "/" . $file)) {
                    reference_dir($path . "/" . $file, $functions);
                } else {
                    if (substr($file, - 4, 4) != ".php") continue;
                    reference_file($path . "/" . $file, $functions);
                }
            }
        }       
    }
    function reference_file($path, &$functions) {
        $tokens = token_get_all(file_get_contents($path));
        for ($i = 0; $i < count($tokens); $i++) {
            $token = $tokens[$i];
            if (is_array($token)) {
                if ($token[0] != T_STRING) continue;
                if ($tokens[$i + 1] != "(") continue;
                $functions[$token[1]][1][] = array($path, $token[2]);
            }
        }
    }
?>

我可能会花更多时间，以便可以快速找到函数定义和引用的文件和行号。该信息正在收集，只是不显示。