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Those are all good questions:
1. The original site had both, but was very poor (read, as in horrible) for ecommerce. At the time, ecommerce was still pretty crude.
2. We got a Yahoo store for ecommerce. It needed a different URL to start setup, so we decided to seperate the commercial and non commercial sites.
3. At that time (1999), Yahoo stores had very poor integration with "normal" websites (as of Dec 2002, they finally have a solution).
4. Yahoo stores had some rather low limits on the size of files and pages, making it impossible to put much of the information on the Yahoo site, since we have over 300 meg just in PDF files.
5. We have had the original domain name since ODP was the Gnu project, and it has hundreds of incoming links, giving it a much better PR on Google than nearly any other competing site.
In fact, we are working on ways to integrate the two sites while keeping both domain names.
However, none of that is the real issue. The major issue is why have we been penalized for two years over our competitors simply because I am an EX-editor?
"They cover the same topic.."
Yes, just as do many other listings in DMOZ that have far more than we do. What justifies Epinion having nearly 2000 - they all cover the same topic..?
And BTW, using fraternal mirror dmoz without quotes only turns up one more relevant site ;p
The major issue is why have we been penalized for two years over our competitors simply because I am an EX-editor?
You haven't been penalized. One of your sites is considered a fraternal mirror of the site already listed. It has absolutely nothing do with the fact that you're an ex editor.
Your site is listed here [directory.google.com].