I've successfully followed some instructions online to get our plain url to direct to the content found in a subfolder (drupaldev) so that when you enter any url for that site even without the subdirectory name, it serves the correct page. However, I cannot figure out how to remove the internal links on the site that reference the '/drupaldev/' subdirectory.

This is what my .htaccess file includes:

RewriteRule ^$ drupaldev/index.php [L]
RewriteCond %{DOCUMENT_ROOT}/drupaldev%{REQUEST_URI} -f
RewriteRule .* drupaldev/$0 [L]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule .* drupaldev/index.php?q=$0 [QSA]

And this is what my settings.php file contains:

$base_url = 'http://www.bluewaterfederal.com'; 

As you can see, if you mouse over any of the links within the site, they all mention drupaldev, but if you take that same url and remove the "drupaldev" from it, it works fine...