Flow extractor api change and documentation.

[water-e]

Currently, the flow_extractor takes a directory rather than a file as its input. I would prefer a file path. Additionally, there are no examples of how to use it in the documentation and once we get done this would be nice.

Finally, it would be nice if the extractor could also make use of fluxflags.prop that has been annotated with labels. I would prefer this look like this, though I'm not sure if the familiar part is possible/wise.

!!!! Labels of flux groups [do not edit this line or below] !!!
12345 ! Old River at Head