Sean Corfield has a blog entry explaining how to extend a root Application.cfc.
Below is the relevant information copied from that entry.
Here's your root CFC /Application.cfc:
<cfcomponent>
<cfset this.name = "cf7app" />
<cfset this.sessionmanagement = true />
</cfcomponent>
Here's your proxy CFC /ApplicationProxy.cfc:
<cfcomponent extends="Application">
</cfcomponent>
It's completely empty and serves merely to create an alias for your root /Application.cfc. Here's your subdirectory CFC /app/Application.cfc:
<cfcomponent extends="ApplicationProxy">
<cffunction name="onSessionStart">
<cfoutput><p>app.Application.onSessionStart()</p></cfoutput>
<cfset session.counter = 0 />
</cffunction>
<cffunction name="onRequestStart">
<cfoutput><p>app.Application.onRequestStart()</p></cfoutput>
<cfdump label="application" var="#application#"/>
</cffunction>
</cfcomponent>
The root of each individual site should have its own Master App:
/site1/Application.cfc
/site2/Application.cfc
/site3/Application.cfc
All these applications are separate individual apps with nothing shared between them.
If any of these individual sites need to have sub-applications, then there should be ApplicationProxy.cfc alonside the Master,
e.g.
/site1/ApplicationProxy.cfc
/site2/ApplicationProxy.cfc
Then, for each sub-application you have the one that extends the proxy:
e.g.
/site1/subA/Application.cfc
/site1/subB/Application.cfc
/site2/subA/Application.cfc
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