<IfModule mod_rewrite.c>
  RewriteEngine On
  RewriteBase /path/to/index/file/

  # Removes index.php from ExpressionEngine URLs
  RewriteCond %{THE_REQUEST} ^GET.*index\.php [NC]
  RewriteCond %{REQUEST_URI} !/system/.* [NC]
  RewriteRule (.*?)index\.php/*(.*) path/to/index/file/$1$2 [R=301,NE,L]

  # Directs all EE web requests through the site index file
  RewriteCond %{REQUEST_FILENAME} !-f
  RewriteCond %{REQUEST_FILENAME} !-d
  RewriteRule ^(.*)$ path/to/index/file/index.php/$1 [L]
</IfModule>