Ja bih ti preporučio da staviš u root folder, da ne komplikuješ.
PHP kôd:
# Turn on URL rewriting
RewriteEngine On
# Installation directory
RewriteBase /kohana/
# Protect application and system files from being viewed
RewriteRule ^(application|modules|system) - [F,L]
# Allow any files or directories that exist to be displayed directly
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
# Rewrite all other URLs to index.php/URL
RewriteRule .* index.php?kohana_uri=$0 [PT,L,QSA]