Google today made a change to the link data in Webmaster Tools that present your backlinks in a way that more closely aligns with your idea of which links are actually from your site vs. from other sites. Today's update won't change your total number of links," announced Susan Moskwa, Webmaster Trends Analyst.
Moskwa explains that "You can manage many different types of sites in Webmaster Tools: a plain domain name, a subdomain, or a domain with a subfolder path. Previously, only links that started with your site's exact URL would be categorized as internal links: so if you entered www.example.com/users/catlover/ as your site, links from www.example.com/users/catlover/profile.html would be categorized as internal, but links from www.example.com/users/ or www.example.com would be categorized as external links."
"This also meant that if you entered www.example.com as your site, links from example.com would be considered external because they don't start with the same URL as your site (they don't contain www)," Moskwa said.
Moskwa writes that Most people think of example.com and www.example.com as the same site these days, so "we're changing it such that now, if you add either example.com or www.example.com as a site, links from both the www and non-www versions of the domain will be categorized as internal links."
However, "if you own a root domain, your number of external links may go down with this change; this is because, as described above, some of the URLs we were previously classifying as external links will have moved into the internal links report. Your total number of links (internal + external) should not be affected by this change," noted Moskwa.
Google also, extended this to include other subdomains--so links from cats.example.com or pets.example.com will also be categorized as internal links for www.example.com.
"If you own a site that's on a subdomain or in a subfolder and don't own the root domain, you'll still only see links from URLs starting with that subdomain or subfolder in your internal links, and all others will be categorized as external links," added Moskwa.