Why are there so many Java files in my "All My Files" section in Finder
In Eclipse preferences choose whether to auto-save or not.

Instructions found here http://help.eclipse.org/luna/index.jsp?topic=%2Forg.eclipse.jdt.doc.user%2Freference%2Fpreferences%2Frun-debug%2Fref-launching.htm

and here
http://eclipsesource.com/blogs/2012/10/26/top-10-tips-how-to-be-more-productive-with-the-best-ide/