Since your site is not in the root of the ananthp.imtqy.com/ domain, but in the "directory" carnatic_scores /, you must set the baseurl variable in the _config.yml file.
baseurl: '/carnatic_scores'
Edit: some explanation
In _includes / head.html you can see this:
<link rel="stylesheet" href="{{ "/css/main.css" | prepend: site.baseurl }}">
which is equivalent
<link rel="stylesheet" href="{{ site.baseurl }}/css/main.css">
baseurl set to " (default) your relative url /css/main.css , which is resolved as http://ananthp.imtqy.com/css/main.css by your browser = 404, is not found.
baseurl set to "/ carnatic_scores" your relative url /carnatic_scores/css/main.css , which is resolved as http://ananthp.imtqy.com/carnatic_scores/css/main.css with your browser = your cool css!
This is true for all assets (css, js and image):
<script src="{{ site.baseurl }}/path_to_scripts/script.js"></script> <img src="{{ site.baseurl }}/path_to_images/image.jpg"> or in markdown 
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