Re: Link checker suddenly reports nearly all links as http://www.domain.com/index.php/en/level1/level2...

I assume that you are talking about your cakephp app or ststic pages as it sis not obvious from your mail at all.

it depends where you have put ur htaccess. I expect u have placed the rule in webroot of your cakeapp, n not in webroot of ur webhosting. surely this rule is overriding some link from other url rewrite to cakeapp webroot 
there is some rewrite rule in some other htaccess, or in httpd.conf  which is sending the requests through this rule

 RewriteCond %{REQUEST_FILENAME} !-d

    RewriteCond %{REQUEST_FILENAME} !-f

    RewriteRule ^(.*)$ /index.php?url=$1 [QSA,L]

tht means index.php got aldeady added to ur url, n before it reaches cake index.file to be directed to page controller or other controllers, its been rewritten to ur new url with all the value in ur $1.

 Remove other htaccess if they are not required. Or simply add [L] flag in the rule  in that htaccess file!!

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