Installing and upgrading help

It disappears because files beginning with a . are hidden. you have to do

ls -al

to see them, that's all.

You *still* have a badly misconfigured server which will make it very hard to debug the problem. You should not get an internal server error just because of missing files. Another thing... if your Moodle install is under /courses then...

home/dharmak/public_html/.htaccess

....is not part of your Moodle install, so I can't imaging how you got there. I'm running out of sensible suggestions Perhaps you should post your config.php file here and keep looking at your error logs to see if anything shows up.

Failing all that, if remote access is available you are welcome to contact me privately and I will have a quick look myself.