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A user, if the website is designed properly, does not have to enter it through the homepage (unless there is a need to have a strong disclaimer ticked).
If the website employs Flash it could fall into two categories. One that the website is essentially one page containing a Flash movie, or two that the navigation links are in a Flash movie modularly combined within an html website. Category one means that much more emphasis has to be placed on the one page website being highly visible through links from other websites. Category two can be assisted by employing the trusty old sitemap page, a small link somewhere in html on every page, which links to a page containing html links to all pages.
In general though, using Flash makes it more difficult to SEO (Search Engine Optimise) the website unless care is taken. A good idea is still to have an html mirror of a Flash website. What is lost in interactivity is gained through the PageRank advantages. As long as there is a link out of any html page to the Flash version of the website, then all bases can be pretty much covered.
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