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As for link popularity you may want to limit the number of links one site can give another. So if a site has 10 pages the most it can give is 1 link. 100 page then 2 links, 200 pages can give 3 links.
I made an advanced SE with a coder and created the user interface. It was aimed at the education industry and we had our own spider. Link popularity was not used because it was not needed. After all the only sites in the directory are non-commercial research and education sites. We chose to ditch the effort because we could not afford to spend time on it though people did use it for 2 years.
The idea was you create “research topics” such as you favourite Football team, your are of works, your favourite music by clicking in a few keywords to that group and every day you can go and check a topic or create a new one. Works well if you spider sites like CNN and BBC.
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