When I was trying to install magento2 for development from github, it was showing me 2 repositories
What is the difference between both and which one to be used for my e-commerce projects?
https://github.com/magento/magento2-community-edition has only composer.json which was required to install Magento 2 using composer install command. It is outdated now, and we do not recommend it anymore (still exist for history purpose).
https://github.com/magento/magento2 is full M2 CE source code, which you can clone and install.
Also there is recommended way to install just to use the composer command
composer create-project --repository-url=https://repo.magento.com/ magento/project-community-edition <installation directory name
For more reference go here - http://devdocs.magento.com/guides/v2.0/install-gde/continue.html