I was able to successfully click on github pages using the command
angular-cli-ghpages --repo=https://github.com/parthghiya/testrepo.git --name=parthghiya --email=parth.ghiya@knowarth.com --no-silent
Repo link: https://github.com/parthghiya/testrepo
I did ng build --prod --base href .
The steps I took:
- Generated my SSH and added it.
https://help.github.com/articles/connecting-to-github-with-ssh/
- The push command is executed.

Edit:
To add multiple folders
Create a folder parallel to the resources, I created 2 folders Parth and Ghiya. Then added the following entry in angular-cli.json
"assets": [ "assets","parth","ghiya", "favicon.ico", "manifest.json" ],
So, the dist folder now contains 3 folders, now assets, parth and ghiya. Then I executed the above push command as before.
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