You should not be bothered about markup indentation in the production environment. Neither should you use Tidy or other HTML purifiers. There are valid use cases, e.g. when you allow HTML input (but consider using Markdown instead), though these are rare.
Most often HTML beautifiers-filters are abused to hide the underlying issues with the code. Don't. Correct your markup manually.
If you need to indent your code only in the development environment, you can use either of the above. However, beware that these libraries will attempt to fix your markup (that's their primary purpose; indentation is a by-product). I've written Regular Expression based indentation tool Dindent.
Dindent will convert markup like this:
<!DOCTYPE html>
<html>
<head></head>
<body>
<script>
console.log('te> <st');
function () {
test; <!-- <a> -->
}
</script>
<div>
<script src="//ajax.googleapis.com/ajax/libs/jquery/1.7.1/jquery.min.js"></script>
<div><table border="1" style="background-color: red;"><tr><td>A cell test!</td>
<td colspan="2" rowspan="2"><table border="1" style="background-color: green;"><tr> <td>Cell</td><td colspan="2" rowspan="2"></td></tr><tr>
<td><input><input><input></td></tr><tr><td>Cell</td><td>Cell</td><td>Ce
ll</td></tr></table></td></tr><tr><td>Test <span>Ce ll</span></td></tr><tr><td>Cell</td><td>Cell</td><td>Cell</td></tr></table></div></div>
</body>
</html>
To this:
<!DOCTYPE html>
<html>
<head></head>
<body>
<script>
console.log('te> <st');
function () {
test; <!-- <a> -->
}
</script>
<div>
<script src="//ajax.googleapis.com/ajax/libs/jquery/1.7.1/jquery.min.js"></script>
<div>
<table border="1" style="background-color: red;">
<tr>
<td>A cell test!</td>
<td colspan="2" rowspan="2">
<table border="1" style="background-color: green;">
<tr>
<td>Cell</td>
<td colspan="2" rowspan="2"></td>
</tr>
<tr>
<td>
<input>
<input>
<input>
</td>
</tr>
<tr>
<td>Cell</td>
<td>Cell</td>
<td>Ce ll</td>
</tr>
</table>
</td>
</tr>
<tr>
<td>Test <span>Ce ll</span></td>
</tr>
<tr>
<td>Cell</td>
<td>Cell</td>
<td>Cell</td>
</tr>
</table>
</div>
</div>
</body>
</html>
Dindent will not attempt to sanitise or otherwise interfere with your code beyond adding indentation. This is to make your development/debugging easier. Not for production.