base_url should not include myAppFolder it should just be your domain name with a trailing /. If your index.php is not in a folder in the bundle you are pushing, go to you EB config -> software configuration and set the following;
document root: /
environment properties: key CI_ENV value production
On the server this is where your files are:
/var/app/current/index.php
/var/app/current/.htaccess
/var/app/current/myAppFolder
/var/app/current/myAppFolder/system
...
Apache serves /var/app/current + your document root set in the control panel.
