To understand how Magnolia has to be setup, it is important to understand the concept of instances.
As you may have heard or read, you need to run a so called "Author" and a "Public" instance. Understanding
why there are two or more instances helps you understand the "Activation process" a lot better.
There are three major reasons, why Magnolia usually uses two different instances:
Once you have developed your Web application and Authors have added the according content, you have
to make the result visible to the Public. That's where the so called "Activation process" comes in.
"Activation" means that you "copy" content from one repository to the other. That's all.So you don't
have to worry about the repositories and protocols.
But since your scripts are NOT in the repository, you will have to copy them manually to the Public instance.
Remember: Your scripts are used to create the response to the browser, so your scripts have to be in each
instance you plan to use.
Please read 'Activation - Subscribers' carefully. It's full of interesting information around "Activation".