Some updates

Dear Gael,

I have fixed the jacobian.py file. You were accidentally called the 'a' vector as 'P', and then used P both for calculating DP and ahat. So I created 'a' and 'P' properly and used them correctly. Also when creating the ahat matrix, you used identity instead of zeros.

I'm not sure about the jacobian transposition part.

I also put some comments for chain and read_par, and did the TODO part of test_jacobian

Matthias