First draft of a ProcessorPipeline

[pckroon]

I had a first stab at making a ProcessorPipeline. I've set it up so that it is a proper recursive DiGraph, but with a convenient .add method. I've also mashed it into bin/martinize2, probably breaking quite a bit of functionality in the process.

There is a lot of logic in bin/martinize2. Some of it is unpacking CLI args (which is fine-ish), some of it is error checking (also fine), but part is also things like writing debug output pdb files. Things like the latter should be squeezed into processors.

Please have a look at it to see if you like the direction. I need to brood on it for a little bit before continuing.