I don’t know if this might be a bug.
This is the code I have before indentation (html5 doctype):
    <ul>
          <li><a href="../docs/introduction.html">Introduction</a>
          <li><a href="../docs/options.html">Options</a>
          <li><a href="../docs/methods.html">Methods</a>
    </ul>    And after indentation I get:
		<ul>
			<li><a href="../docs/introduction.html">Introduction</a>
				<li><a href="../docs/options.html">Options</a>
					<li><a href="../docs/methods.html">Methods</a>
		                        </ul>				It seems ST2 has problems with open tags in html5 syntax