Updated the "Examining the MDL" section.

There is no longer a need to annotate the MDLs (at least in this
example), since CellBlender generates the visualization and reaction
data now. The directory and file names needed updating too, since we
changed our policy on how these are created.
Updated a slightly inaccurate file name.

Now that there are no hand-edited changes to the MDLs in this section,
the "annotate" in "examine_annotate.rst" was no longer accurate and
needed updated.
Updated the "Visualize and Plot" section.

The video and some of the plotting information was commented out, since
it was out-of-date.

The **Visualize Simulation Results** panel has changed, so that section
was updated.

Also, it was pretty hard to see the glyphs because they were so small,
so I added a section where the user scales them up (along with some
pictures).