Figures in Atlas is straight up HTML:
<figure id="figure1-1">
<img src="../../figures/18333fig0101-tn.png"/>
<figcaption>Local version control diagram.</figcaption>
</figure>
Internal links in documents can be created with the hash syntax:
<a data-type="xref" href="#rebase-example">My Link</a>
<figure id="rebase-example">
You should use GFM for tables.
Use data-type="note"
for notes:
<div data-type="note">
<span class="notelabel">Note</span>
Note text!
</div>