Collocated unified cov scheme

[yairchn]

Includes changes followed by the Soares test case:

1. consistent sign of entr_term in the massive detainment applied for a>au_lim and in compute_covariance_entr and compute_covariance_detr functions.
2. the are fraction limiter and the clipping (commented for now) are inside upwind_integration
3. slight chanegs to the GATE_II case in Cases.pyx (it is running now but still not working properly)
4. "_c" replaced "_half" and "_f" is added to instead variables on full levels . yet in the output name it is till z and z_half just so the travis tests will work