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My boss said something about our content not being crawled fully because most of our content is in /pages/
Therefore many of the URLs look like (and this is not a real URL)
www.nameofcompany.com/pages/filename.htm
Is he right? Should I move all my content to the root directory?
Make sure you have a robots.txt file and it is valid. The SearchEngineWorld robots.txt validator page [searchengineworld.com] has links to additional information.
Check that pages don't have inadvertent robots noindex meta tags.
Make sure that pages are well-linked so spiders can find them. Consider using a site map to help them along the trail.
Also, if you have any sort of bot blocking going on in your .htaccess file check that it isn't keeping the good guys out.
Try changing the content a bit on some of the pages. Some bots do a conditional GETs and won't retrieve not modified pages. Similarly, try adding a few new links to your index page, bots love to travel new paths.
And, of course, try to pick up some external links to those interior pages.