Add bootstrapping script to remove hardcoded paths

This 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 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

Changes to be committed:
      modified:   .gitignore
      new file:   .gitmodules
      modified:   001-extract-reads-by-coverage/Makefile
      modified:   001-extract-reads-by-coverage/index.rst
      modified:   002-collect-subset-of-high-coverage/Makefile
      modified:   002-collect-subset-of-high-coverage/index.rst
      modified:   003-estimate-genome-size/Makefile
      modified:   003-estimate-genome-size/index.rst
      modified:   004-estimate-sequencing-saturation/Makefile
      modified:   004-estimate-sequencing-saturation/index.rst
      modified:   005-estimate-total-genome-size/Makefile
      modified:   005-estimate-total-genome-size/index.rst
      modified:   006-streaming-sequence-trimming/Makefile
      modified:   006-streaming-sequence-trimming/index.rst
      modified:   007-variable-coverage-trimming/Makefile
      modified:   007-variable-coverage-trimming/index.rst
      new file:   bootstrap.sh
      new file:   khmer
      new file:   literate-resting
      new file:   nullgraph
Update bootstrapping to rm submodules, + git clone

I've removed the git submodules of dependencies, and made bootstrap.sh
git clone the repos at runtime
Check for repos before git-cloning in bootstrap.sh
Add bootstrapping process to makefile

Added under all 'recipes' target