How much customization are you talking about? Do you just want to change the banner at the top of the page and/or the color of the "background" or do you want to do more extensive changes?
No unfortunately I want to loose the whole folder structure and a few separate areas where you could see new reports, reports just for you, documentation, etc. It should look more like a regular web page.
This is a huge amount of work. You're better to think of what you're trying to do as a portal integration project. Rather than customizing BO, build your own portal and make calls in to the BO API for the display.
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