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1.What can I do to get the main directories out of penalty again so that they spread their PR power to the rest of the pages?
2.Are the deeper sub-pages able to pass any PR to pages they link to or are they stigmatized because of their connection with the main directory?
Any examples of how you got out of this penalty or any insight you have on this issue in general would be much appreciated.
The reports of improvement that we've seen include these steps -
1. remove all links to bad external neighborhoods
2. make it obvious that your directory puts submissions through a true editorial review
3. never suggest that your listing will improve Google rankings
So I guess I'm wondering why you think it's a penalty and not just a change in the PageRank calculation.
Depending on what the infractions were, Google may not respond at all, or they may remove the penalty in slow stages. Sometimes, you get lucky and things bounce back quickly. The key is remembering that you may be under human editorial scrutiny, so don't try to "slip anything past". Go as squeaky clean as you possibly can be before requesting reconsideration.
make it obvious that your directory puts submissions through a true editorial review
I think you misunderstood what I meant by directory. We have an e-commerce site, we are not a directory that lists sites. I meant "directory" in the site architecture sense:
"red-widgets" being the directory. We barely have any outbound links.
If you know what you did wrong in the past, then undo every trace of it that you can
Easier said than done, lol. But I guess that's what we were afraid of. A reinclusion request is probably not the way to go for us at this point. It will take a long time to "undo every trace", and the fact is that some parts of our site are doing very well.
It makes more sense for us to slowly clean up our site, and hope that this penalty wears off over time. Great inbound links still work great on individual pages, but with over 20k pages on the site its just impossible to get an IBL for every page.