Running wordpress from subdirectory css url path issue (thesis child)

I am finishing off developing a site in a directory (root/wordpress/). I then wanted to run it from the root so followed the wordpress documentation which involved changing the site address but not the wordpress address and copying the index.php and .htaccess file from my /wordpress/ directory to the root. I have done this with other sites before without issue.

On this particular site it kind of worked. The home page was there and I could get into the admin – but none of the css loaded for the front end or for the admin. When I looked at the source code all the css and js references in the head section were referenced as being in the root rather than the /wordpress/ directory so of course were not being found.

I can’t seem to find this issue reported anywhere or solve it myself. I am thinking someone hard coded a line or variable they should not have when they set up the thesis child theme.

Can anyone tell me how the logic flows through from the database through to the setting.php file and then the thesis files that set where the blog url is so I can check none have been changed?