There may be slightly more reason to lean towards using subdirectories but each case is different. Have you looked these over yet:
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Best posts made by Chris.Menke
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RE: Sub-domains or sub-directories for country-specific versions of the site?
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RE: Local SEO: Can you add citations too fast?
Hey Bob,
It's not something you hear much about and certainly not something I've considered in doing work for many local clients, but I think I hear what you're saying. Typically, I'd go to UBL.org, choose a package for the client, let the citations start flying, and be glad that it getting done as quickly as possible-- without even thinking about velocity.
I went over to David Mihm's 2012 local search ranking factors, and looked specifically for info on that and interestingly, that's not mentioned as a factor (which might be why I'd never given it a thought.)
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RE: My website disappears off google!
Becca,
That wouldn't be too strange if it's very new and since you say that you're building it, I assume that it is. If it's older than a couple of months, it would be strange. Getting some links and some social media activity going for it would probably work to stabilize things for you.
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RE: How to create site map for large site (ecommerce type) that has 1000's if not 100,000 of pages.
Typically, a sitemap is going to include every page on the site. As Francesca said, each sitemap can be up to 50K urls and if you need multiple sitemaps then you create a sitemap index that points to the rest of the sitemaps.
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RE: How do you find Affiliate Links on your site that have not been nofollowed?
Actually, screamingfrog should take care of it for you via the custom spider configuration. If you select "custom" under the "configuration" tab, you can drop in the html for the links you are looking for and it will give you a report with what pages it finds that code on.
For example, have screammingfrog search for the following snippet of code and it would find nofollow links pointing at mysite.com:
rel="nofollow" href="http://mysite.com
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RE: Best way to permanently remove URLs from the Google index?
Wouldn't a noindex meta tag on each page take care of it?