codeigniter in a subdirectory, some issues.

Why don't you move your "common" directory outside of "application" ? I think it make more sense to put JS, CSS and images at the root of the web site. And you won't have to mess with htaccess to make your links work.

My index.php is the main culprit. I normally expect to leave the file in the "application" folder. However, when I do that, I dont get my home controller, but instead the site will only load a page that says "index of /2013", and then lists all the files in the root as links:


Parent Directory
   .gitignore
   .travis.yml
   application/
   license.txt
   user_guide/

Why would you move index.php inside application? It is supposed to be outside application. Leave it there! That is exactly why nothing load and you only see a list of files...