<p>Using the SharePoint API, how can I modify an extended webapp web.config file?</p>
<p>I have to do some changes in this file to specify the connection string, membershipprovider, etc... for using Forms Authentication.</p>
<p>Currently, I can change the &quot;master&quot; webapplication web.config file, but not the extended one.</p>
<blockquote>
<p>Edited</p>
<p>I'm using Sp 2007. I'm already using SPWebConfigModification class to modify the parent webapp. Thoses modifications are propagated to the extended webapp. I have to change ONLY the extended one. But I don't find the way to do it.</p>
<p>What I'm trying to achieve, is to program a little wizard that:</p>
<ul>
<li>Shows a WebApp list so the user can select one</li>
<li>Extend that selected webapp to a different zone</li>
<li>Configure that extended zone to use Forms Authentication</li>
</ul>
</blockquote>
<p>Thanks</p>

Quick answer: look into the SPWebConfigModification class. I am assuming you're using SharePoint 2007. The best way to learn about this is to dig into open source projects:
Google code search:
http://www.google.com/codesearch?q=spwebconfigmodification&hl=en&btnG=Search+Code
This project on CodePlex looks like it's one big SPWebConfigModification:
http://www.codeplex.com/ajaxifymoss/Release/ProjectReleases.aspx?ReleaseId=13360