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    <p>I have WordPress in the root directory and my CodeIgniter application in a sub-directory. I create a similar <code>web.config</code> like yours and save it in the sub-directory. My CI app doesn't need the index.php in url any more.</p> <p>At first, I add my sub-directory in the <code>&lt;action url="myapp/index.php/{R:1}"...&gt;</code> and wish it could be restricted to look into the sub-directory only but fails. I remove the sub-directory and leave it to original but move the web.config to the subdirectory and it works.</p> <p>Therefore, I think maybe you may create two web.config files with different rules and saves them in different directory.</p> <p>Another note might help: enable the error message to output the detail from IIS. I use the tricks to find out how IIS looks for my files. It is <code>&lt;httpErrors errorMode="Detailed" /&gt;</code>, <code>&lt;asp scriptErrorSentToBrowser="true"/&gt;</code>, and the <code>&lt;system.web&gt;</code> section as below:</p> <pre><code>&lt;?xml version="1.0" encoding="UTF-8"?&gt; &lt;configuration&gt; &lt;system.webServer&gt; &lt;httpErrors errorMode="Detailed" /&gt; &lt;asp scriptErrorSentToBrowser="true"/&gt; &lt;rewrite&gt; &lt;rules&gt; &lt;rule name="RuleRemoveIndex" stopProcessing="true"&gt; &lt;match url="^(.*)$" ignoreCase="false" /&gt; &lt;conditions&gt; &lt;add input="{REQUEST_FILENAME}" matchType="IsFile" ignoreCase="false" negate="true" /&gt; &lt;add input="{REQUEST_FILENAME}" matchType="IsDirectory" ignoreCase="false" negate="true" /&gt; &lt;/conditions&gt; &lt;action type="Rewrite" url="index.php/{R:1}" appendQueryString="true"/&gt; &lt;/rule&gt; &lt;/rules&gt; &lt;/rewrite&gt; &lt;/system.webServer&gt; &lt;system.web&gt; &lt;customErrors mode="Off"/&gt; &lt;compilation debug="true"/&gt; &lt;/system.web&gt; &lt;/configuration&gt; </code></pre> <p>Wish it help!</p>
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