I first installed WP into a sub directory of my website as a "news" blog. Now I am installing on root and will use as a CMS. My news blog has many index pages with google etc, so my plan was to make a category called "news" and all my category's would then be childs of "news". So my urls would look like mydomain.com/news/category/post/.
This seemed to work fine when navigating to a post, however, when clicking on category links it takes me to /mydomain.com/category/news/subcat/post/.
I tried removing code in classes.php etc which only resulted in 404's. All the hacks and tricks I have found do not work with my setup, they either require a .html extention on the url, or do not work with childs category's.
I could really use help, do not want to loose indexed pages or have a non-logical architecture.
My permalink structure is %category%/%slug% and I am running wp 2.7.
If you are a pro, I can kick you down some cash via paypal donate.