make modules available for easy pull + import

[worden-lee]

I need to find a way to publish the python modules not embedded in .wmd source, so other projects can easily pull and import them.

[worden-lee]

Like this, I think:

• put all .py modules (boxmodels.py, boxkolmogorov.py, etc) into a src/ directory, no longer within .wmd files. Only put downstream code that uses the modules in .wmd files.
• all modules should be .py files, not .py.step. The step formulation isn't useful for these files, and it makes them harder to use, and adds difficulty for third parties.
• ultimately this repo, and the SageDynamics one, should be organized with several parallel sections: the modules (the downstream-useful part) in src/; tests in test/ or such; documentation in doc/ and/or in docstrings within the modules; related material in .wmd files, somewhere but I'm not sure where, maybe including README.md.wmd.

[worden-lee]

the master branch of the repo contains the raw source including .wmd files. There may be a clean way to link to the gh-pages branch for online publication, allowing us to use wmd documents with computation results in them for the documentation, readme, etc.

[worden-lee]

first 2 bullets done