Google Webmaster redirect vs 301 redirect
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OK assuming a client's website has the right tracking script (hopefully analytics isn't effected by this issue),
... what happens if the htaccess file has a 301 redirect to the www-address, but within Google Webmaster Tools, the address chosen to crawl by Google is the non-www address?
How will Google handle and which address takes precedence in this situation?
_Cindy
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More information can be found here regarding this setting and how it is used by Google. It will help answer your question.
https://support.google.com/webmasters/bin/answer.py?hl=en&answer=44231
To be honest though I'd just update the GWT setting or the 301 so they are both the same...