insign/CodeIgniter — comment on commit 5287f6643f5ca55c360a6372c526c8c06c0c4912
File:  line 0
By insign:

Humm, I'm not sure...

See:
My site are in http://localhost/site
The CI are in http://localhost/site and the "application" folder are in /site/application

It match with you affirmation? If yes, why not warned in the user_guide?