Now before you can contribute to Neptune, you need to understand the layout of the project.
NeptuneVanilla:
This is the 'vanilla' Minecraft implementation.
NeptuneForge:
This is the Minecraft Forge implementation.
NeptuneCommon:
This is the shared code, between both NeptuneVanilla and NeptuneForge. This is where the majority of the implementation happens.
You can find details of how NeptuneCommon is laid out in another post