I have multiple websites installed in one Magento, and for one website, I have a full view store(www.example.com) and mobile view store(www.example.com/mobile). I have taken off the index.php from full store, but for somehow, it cannot be taken off from mobile store, I double checked, (1) Use Web server Rewrites set to yes (2) Use secure Url in frontend to yes (3) .htacess Rewrite Engine on and RewriteBase/. I cleared the Magento cache several times and I even reindexed. Why the index.php is still there?
Here is part of .htacess file.
## enable rewrites
Options +FollowSymLinks
RewriteEngine on
############################################
## you can put here your magento root folder
## path relative to web root
RewriteBase /