[javascript] Combine and Minify Multiple CSS / JS Files

I am trying to optimize a site performance by consolidating and compressing the CSS and JS files. My question is more about the (concrete) steps on how to achieve this, given a real situation I was facing (should be typical among other developers too, though).

My page references several CSS and JS files like the following:

<!--
  It's easier to work on smaller files during development.
  Hence, the multiple CSS and JS files.
-->
<link type="text/css" rel="stylesheet" href="/css/main.css" />
<link type="text/css" rel="stylesheet" href="/css/secondary-1.css" />
<link type="text/css" rel="stylesheet" href="/css/secondary-2.css" />

<script type="text/javascript" src="/scripts/js/main.js"></script>
<script type="text/javascript" src="/scripts/js/adapter/adapter.js"></script>
<script type="text/javascript" src="/scripts/js/adapter/title-adapter.js"></script>

For the production release, I'd like to combine the 3 CSS files into one and minify it using e.g. YUI Compressor. But then, I'd need to update all pages that needs these 3 files to reference to the newly-minified CSS. This seems error-prone (e.g. you're removing and adding some lines in many files). Any other less-risky approach? The same issue for the JS files.