Fot the Windows users - have a look at the project templates that I created. You can find them here. https://github.com/mariusl/Eclipse-for-AVR
Place all three projects (ArduinoCore, ArduinoLibraries and Template) in the same workspace. The projects are set up to include the core and libraries from the workspace area. I recompile the libraries when I download or include a new library and this way all items are always current.
Having all the projects in the same workspace makes it very easy.
To include a new library you go to the ArduinoLibrary project. Right click on the project file, click on the Import option, go to the Arduino librarydirectory, select the directory that you want to use, select all the code and header files from the list, make sure that the "create complete folder structure" is selected and away you go.
Now just rebuild the ArdfuinoLibrary project and all is done.