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This is because the spiders will always properly index your homepage as www.example.com and won't have problems if other sub-domains or https types are used by mistake.
"Confused with subdomain" I just don't understand. There is a distinct difference between
However, FROM a subdomain,
will return to
Which is actually an ease of maintenance issue, you can move the page from the domain to the subdomain without changing links.
But the search engines will still see it as http://widgets.example.com.
Typical examples of where you want to use the FULL url:
<a href="https://example.com/login/">Log in</a>
From secure pages, to get OFF https and allow the site to run faster,
<a href="/login">Log in</a>
[edited by: phranque at 7:57 am (utc) on April 22, 2009]
[edit reason] unlinked urls [/edit]