If you have a lot of virtual applications under your webiste
You can Disable the main website's web config so it won't inherit to your Virtual Application.
It's quite simple about how to disable this Web Config's inheritance. All you have to do is simply modify your Web config with a <location> tag. The <location> tag can prevent inheritance for part of the web config.
<?xml version="1.0"?>
<configuration>
<configSections>
....
</configSections>
<location path="." inheritInChildApplications="false">
<appSettings>
....
</appSettings>
<connectionStrings/>
<system.web>
....
</system.web>
<system.codedom>
....
</system.codedom>
<system.webServer>
....
</system.webServer>
</location>
<runtime>
....
</runtime>
</configuration
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