In order for Drupal's Clean URLs to work, replace the .htaccess file created with the following:
# Protect files and directories from prying eyes.
<FilesMatch "(\.(engine|inc|install|module|sh|.*sql|theme|tpl(\.php)?|xtmpl)|code-style\.pl|Entries.*|Repository|Root)$">
Order deny,allow
Deny from all
</FilesMatch>
# Set some options.
Options -Indexes
Options +FollowSymLinks
# Set the default handler.
DirectoryIndex index.php
php_value magic_quotes_gpc 0
php_value register_globals 0
php_value session.auto_start 0
# Reduce the time dynamically generated pages are cache-able.
<IfModule mod_expires.c>
ExpiresByType text/html A1
</IfModule>
<IfModule mod_mime.c>
AddCharset utf-8 .html
</IfModule>
RewriteCond %{REQUEST_URI} !^/cache
RewriteCond %{REQUEST_URI} !^/user/login
RewriteCond %{REQUEST_URI} !^/admin
RewriteCond %{HTTP_COOKIE} !DRUPAL_UID
RewriteCond %{REQUEST_METHOD} ^GET$
RewriteCond %{QUERY_STRING} ^$
RewriteCond %{DOCUMENT_ROOT}/cache/%{SERVER_NAME}/0/%{REQUEST_URI} -d
RewriteCond %{DOCUMENT_ROOT}/cache/%{SERVER_NAME}/0/%{REQUEST_URI}/index.html -f
RewriteRule ^(.*)$ cache/%{SERVER_NAME}/0/$1/index.html [L]
RewriteCond %{REQUEST_URI} !^/cache
RewriteCond %{REQUEST_URI} !^/user/login
RewriteCond %{REQUEST_URI} !^/admin
RewriteCond %{HTTP_COOKIE} !DRUPAL_UID
RewriteCond %{REQUEST_METHOD} ^GET$
RewriteCond %{QUERY_STRING} ^$
RewriteCond %{DOCUMENT_ROOT}/cache/%{SERVER_NAME}/0/%{REQUEST_URI}.html -f
RewriteRule ^(.*)$ cache/%{SERVER_NAME}/0/$1.html [L]
# BOOST END
# Rewrite current-style URLs of the form 'index.php?q=x'.
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(.*)$ index.php?q=$1 [L,QSA]
