The code presumably doesn't need tweaking. Or at least not supposed to. What you need to set up is mostly your build environment and your mozconfig.

For MerSDK - see https://wiki.mozilla.org/How_To_Buil...c_with_Mer_SDK
For Harmattan you need to use its own SDK: https://wiki.mozilla.org/How_To_Buil..._Harmattan_SDK

I think Harmattan SDK in general isn't maintained anymore (so don't expect tools upgrades there - it's in the frozen state). It's basically Nokia's legacy build system.

Mer SDK is updated regularly - Mer is not associated with Nokia, it's a community project. Jolla's Sailfish is based on Mer, so you will be able to use Mer SDK for it as well.

If you are a bit fuzzy about history, here is the short version:
Nokia had Maemo project, which they decided to merge with Intel's Mobiln. They created the Meego project. Meanwhile they released N9 with Harmattan OS, which isn't exactly Meego, but it's their Maemo in transition to Meego (in some intermediate state which is really closer to Maemo than to Meego). After that Nokia basically dropped the whole thing. Community forked some parts of Meego (not Harmattan - that's important), and created a Mer project which is a core distribution. Now other projects like Nemo (which also inherits Meego Handset subproject), Plasma Active and Sailfish use Mer as their base.

So on N9 you can either run Harmattan which Nokia ships with it, or you can install Mer based Nemo OS there. If you use the device only for development and testing, rather than everyday use - I'd recommend using Nemo, since you essentially train how to use Mer SDK and it'll be helpful for the upcoming Sailfish.

But if you use it as your primary device, Harmattan is still probably more useful.