My search engine is running at
http://www-pcmdi.llnl.gov/search/search.php to index
http://www-pcmdi.llnl.gov. I did a clean install and everything works. The only values I changed in the config.php file were to remove the limits from everything, setting all values to "0". I input my URL to have it indexed. It only indexes the first page, but doesn't follow any links to index the rest of the site. I was wondering if this is because my menu is setup in javascript within an ".inc" file, but my static "a href" links don't get followed either. PLEASE HELP!