gistfile1.js

    var data = [],
        html = '',
        slice = Array.prototype.slice,
        navigation = document.querySelectorAll('.navigation')[0];

    // store useful values in the data array
    [].forEach.call(document.querySelectorAll('section'), function(section){
        data.push({
            'filename': section.dataset.filename,
            'h1': section.querySelectorAll('h1'),
            'h2': section.querySelectorAll('h2')
        });
    });

    html += '<ul>';

    // loop trought data array and add up string in the html string
    data.forEach(function(obj){
        var h1 = slice.call(obj.h1),
            h2 = slice.call(obj.h2);
        
        h1.forEach(function(node) {
            html += '<li><a href="#' + node.id + '">' + node.innerHTML + '</a>';
        });

        if (h2.length > 0) {
            html += '<ul>';

            h2.forEach(function(node) {
                html += '<li><a href="#' + node.id + '">' + node.innerHTML + '</a></li>';
            });

            html += '</ul>';
        }

        html += '</li>';
    });

    html += '</ul>';

    navigation.innerHTML = html;