We've created an apps global.jsp that will load the version in the /libs folder as well as other custom jsp files we've created. So the fist include section of all of our components looks something like this:
When we create a new component, CQ automatically inserts the default libs version:
Is there a way to change CQ so that the default include is our apps version and not the /libs default version? We are using 5.5 Update 1
You will be modfying the file anyway to implement logic better to have in your checklist and modify that include also.
On 5.3/5.4 modify the method getJspContent at location . For 5.5 need to download the bundle  , extract modify the file CreateComponentAction.js and install it from felix console.
 <cq_home>/crx-quickstart/server/runtime/0/_crx/docroot/de/js/CRX/plugins/action/CreateCom ponentAction.js