domain is redirected to suddirectory by mod_rewrite but cakePHP is messing up urls

I currently have my main domain being redirected from the root directory to a subdirectory. And because of this every time I use cakePHP to write urls or get the current one it displays the subdirectory.

for example: If I am at the home page (http://example.com) and then use cake's $this->url it will return /mysubdirectory/

here is the .htaccess file I used (of course modified to fit my needs) in my root directory that redirects to a subdirectory.

# Hostmonster.com
# .htaccess main domain to subdirectory redirect
# Copy and paste the following code into the .htaccess file
# in the public_html folder of your hosting account
# make the changes to the file according to the instructions.
# Do not change this line.
RewriteEngine on
# Change yourdomain.com to be your main domain.
RewriteCond %{HTTP_HOST} ^(www.)?yourmaindomain.com$
# Change 'subdirectory' to be the directory you will use for your main domain.
RewriteCond %{REQUEST_URI} !^/subdirectory/
# Don't change this line.
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
# Change 'subdirectory' to be the directory you will us开发者_如何学编程e for your main domain.
RewriteRule ^(.*)$ /subdirectory/$1
# Change yourdomain.com to be your main domain again.
# Change 'subdirectory' to be the directory you will use for your main domain
# followed by / then the main file for your site, index.php, index.html, etc.
RewriteCond %{HTTP_HOST} ^(www.)?yourmaindomain.com$
RewriteRule ^(/)?$ subdirectory/index.php [L]

I feel like I need to modify the .htaccess files in side my cakePHP app to ignore the subdirectory but I'm unsure how.

did you add

RewriteBase /subdirectory/

in your .htaccess in the directory where your /app and /cake folders are placed?