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I think that multiple options can be used in your scenario.
If you are going to create a close portal, may be you would like to start from the examples portal (classic) and modify it.
Another option is to use an extension, for example, the mobile part is created as an extension, this give you an idea about how to create your custom portal and deploy it as a single .ear.
Also you can take a look into the code:
A good start point about extensions is to take a look into the quickstarts, there is one covering extensions topics:
Hope this helps to give you some ideas about personalization of your portal platform.
I think that it will depends of your whole scenario, if you are creating a portal where third party teams can write portlets and applications, or if you are creating a single application that uses a portal embedded.