How do I set up Eclipse/EGit with GitHub?

Make sure your refs for pushing are correct. This tutorial is pretty great, right from the documentation:

http://wiki.eclipse.org/EGit/User_Guide#GitHub_Tutorial

You can clone directly from GitHub, you choose where you clone that repository. And when you import that repository to Eclipse, you choose what refspec to push into upstream.

Click on the Git Repository workspace view, and make sure your remote refs are valid. Make sure you are pointing to the right local branch and pushing to the correct remote branch.

In Eclipse, go to Help -> Install New Software -> Add -> Name: any name like egit; Location: http://download.eclipse.org/egit/updates -> Okay. Now Search for egit in Work with and select all the check boxes and press Next till finish.

File -> Import -> search Git and select "Projects from Git" -> Clone URI.In the URI, paste the HTTPS URL of the repository (the one with .git extension). -> Next ->It will show all the branches "Next" -> Local Destination "Next" -> "Import as a general project" -> Next till finish.

You can refer to this Youtube tutorial: https://www.youtube.com/watch?v=ptK9-CNms98

Install Mylyn connector for GitHub from this update site, it provides great integration: you can directly import your repositories using Import > Projects from Git > GitHub. You can set the default repository folder in Preferences > Git.