Automatic in-page navigation plugin?
If I'm understanding you correctly, you want users when they visit your site to have a secondary menu that has links to various points in the article. That would actually be very easy to do in Craft. It's also possible for you to paginate a page, but that would be far more in-depth.

For skip links, you would need to run over the matrix twice. You will also need an anchor matrix block. It can either be a dedicated block for anchor tags, or a header block. You run over it the first time to create your menu:

&lt;ul class="article menu"&gt;
{% for block in entry.articleMatrix.type('header') %}
    &lt;li&gt;&lt;a href="#{{ block.header|slugify }}"&gt;{{ block.header }}&lt;/a&gt;&lt;/li&gt;
{% endfor %}
&lt;/ul&gt;


Then later when you are running over your article, you can check for block type and add the id as needed:

{% if block.type == "header" %}
    &lt;h1 id="{{ block.header|slugify }}"&gt;{{ block.header }}&lt;/h1&gt;
{% endif %}


This is a really basic example. It uses Bob Olde Hampsink's slugify plugin (it uses Craft's built in slug method). It would be better if you could determine (maybe with a drop down field in your block) what level of heading the block is. I suggest you also cache each matrix loop for performance.