The first stage in updating the manual to stage 4.1.1 - making sure that I
can add files to github.
Starting update to Stage 4.1.1

Starting a manual update to Stage 4.1.1, with more example code and
instructions.
Rearranging in preparation for new example code
Added example code for each step in the tutorial.
Update of examples code to match manual.
A bibliography for the manual.
With show_data on.
Update of manual to version 3 (Stage 4.1.1)
Added some more instructions on how to navigate the example code.
Changed space_invader back to circle.png and added some wording to make the
explication of same more clear.
Merge pull request #1 from knickels/master

manual update to stage 4.1.1 from knickels repository