Please help me, need help getting rid on index.php

I'm using this code to redirect all index files to root

RewriteRule ^index.(.*)?$ http://www.mysite.com/  [r=301]

Code (markup):

Unfortunately every link from linking websites use the following convention "http://mysite.com" which produces "http://www.mysite.com/index.php?" on my end. With my redirect the links end up as "http://www.mysite.com/?" with the question mark following through.

How do i get rid of this damn question mark??????

My entire .htaccess file is below

Options +FollowSymLinks
RewriteEngine On

RewriteRule (.+)\.ht$ shop.php?name=$1 [L]  
RewriteRule (.+)\.html$ auction_details.php?name=$1 [L]  
RewriteRule (.+)\.cfm$ categories.php?parent_id=$1 [L]
RewriteRule ^(.*),(.*)$ $2.php?rewrite_params=$1&page_url=$2

RewriteRule ^index.(.*)?$ http://www.mysite.com/  [r=301]

RewriteCond %{QUERY_STRING} base64_encode.*(.*) [OR] 
RewriteCond %{QUERY_STRING} (<|%3C).*script.*(>|%3E) [NC,OR] 
RewriteCond %{QUERY_STRING} GLOBALS(=|[|%[0-9A-Z]{0,2}) [OR] 
RewriteCond %{QUERY_STRING} _REQUEST(=|[|%[0-9A-Z]{0,2}) 
RewriteRule ^(.*)$ index.php [F,L]

Code (markup):