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my website was hit by bots, so i have moved it to another folder in the same site. 

I added this for redirection : Redirect /index.php http://www.mywebsite.com/folder

Every pages are indexed in google but i m still seeing that mywebsite.com is still being indexed but there is not index.php file in root directory. Is that ok?

It's ok. It might take Google a little time to update your changes with the url; however, I don't think moving the site to a different folder is going to help much with the spam bots (for the long term).