Put everything inside of an eclipse project

Look to these links for the reasons why:
http://programmers.stackexchange.com/questions/202051/what-should-i-include-in-my-repositiory-from-ide-projects
http://stackoverflow.com/questions/17256411/eclipse-setup-for-git-project
http://stackoverflow.com/questions/2818239/classpath-and-project-check-into-version-control-or-not/2819639#2819639