[WIP] Changed Example to Examples to make docstrings process correctly.

Fixes:

1.  "Example" (not Examples) sections in docstrings gives warning, so I changed to examples.


2.  Error below, fixed by removeing ":ref:" from introduction.rst

```
/home/kyleb/src/kyleabeauchamp/mdtraj/docs/examples/introduction.rst:25: WARNING: undefined label: trajectory (if the link has no caption the label must precede a section header)
```