XReliquary (Minecraft Mod) source code.
My packages are structured in virtually the exact same way as Pahimar outlines in his glorious Let's Mod series (which you should watch if you are new to modding, as they are awesome.)
To get started working on the source, you will need to set up an eclipse workspace and point to these directories manually, using linked resource folders. (That's how we did it anyway.) You can pretty much follow his directions to the letter, as I've used his structure as my preferred model of development for the mod.