[WIP] Add bootstrapping script to remove hardcoded paths

**NB: this is work in progress / a proposal**

This PR removes all references to locally installed things (code and
programs) that aren't bundled with the repo. To do this, we add khmer,
literate-resting and nullgraph as git submodules. We also create
./bootstrap.sh, a script that sets up a local virtualenv with khmer and all
dependencies.

Basically, the following should give no errors:

    git clone --recursive https://github.com/ged-lab/khmer-recipies
    bash bootstrap.sh
    for recipie in 00*/ ; do pushd $recipie; make; popd; done


Unfortunately it still doesn't fully work on my machine, and I've not had time to fix it yet. Will do so over the next week or two, and update the PR when it works.