Fix the code to use the correct formulae.

* Use the sign convention and formulae from Milne-Thomson.
* Error was due to ignoring the fact that the z-axis pointed downwards.
* Compute the normal and the rotation using the right sign convention.
* Change the symbol for height from y to z.
* Update all the comments.
Change pi/2 to -pi/2 for the final flight path.
Use 0 as subscript for the initial values.
Merge pull request #22 from anushkrish/master

Fix phugoid.py to use the correct formulae
Merge remote-tracking branch 'upstream/master'