Add HTML titles, logos and icons.

Address #52.

The colors for the logo are #58b91a and #f1d71d
Switch to Bootstrap theme

Address #52

Bootstap theme seems much nicer.

 * remove search box

 * switch to sphinx_bootstrap theme

 * using contents file instead of index

 * reduced size of logo

 * remove copyright
Move master file back to index.rst

Address #52

PyMKS icon can't point at anything other than the master file. Include
the introductory notebook in the master file.
Clean up README.md for webpages.

Address #52

Clean up from page by merging README and IPython notebook in
index.rst.
Clean up intro for front page

Address #52
Merge branch 'master' into issue52-docs
Renname notebooks to have shorter names

Address #52
Clean up docs for front page

Address #52

 * Fix casting warning in FE model.

 * Create functions to render images for front page.
Merge branch 'master' into issue52-docs
Add image for intro notebook.
Switch to Mathjax from PNG images

Address #52

Using Mathjax will take much less space in the repository.
Clean up the installation instructions.

Address #52

 * Other small improvements

 * Removed half finished examples from examples contents

 * Add theory section
Clean up API

Address #52

Not using a scatter gun appoach to building API. Specify each of the
modules instead.
Merge branch 'issue52-docs'

Fix #52