This week's book giveaway is in the OCPJP forum. We're giving away four copies of OCA/OCP Java SE 7 Programmer I & II Study Guide and have Kathy Sierra & Bert Bates on-line! See this thread for details.
That means you can install a JRE and only have the jre contents, or a jdk and have both bin folders. You can also set your PATH to choose with instance of the java tool to use.
On a Windows® box, you would have the same contents, but they would have extensions, so it’s java.exe rather than java.
How do you know they are actually duplicate files, rather than links from one file to another? In my case, they probably are duplicates, but none of them is very large: