Thanks David.
I understood the concept and now I want to change the structure of my application and want to undo the custom javascripts references from portaltemplate.aspx. But on server, any changes to portaltemplate.aspx is not reflecting and I am not able to remove those unnecessary javascripts references from portaltemplate.aspx.
Can you please suggest me how to clean up my portaltemplate.aspx file on server once.
thank you
Ruchika