Updates doc equations

[navidcy]

This PR changes vector notations in docs from the cumbersome and wrongly rendered arrow, e.g., in

to bold notation, e.g.,

Also, the PR fixes a few typos, e.g., definition of Φ was never rendered and equations were not punctuated.

NOTE 1

I believe there is an inconsistency between the "Vector invariant equations" and the "Governing equations". While the w-momentum equation is recovered from the vector invariant equation, the geopotential term in the horizontal momentum equations in the vector-invariant equations` reads as, e.g.,

ρ/ρ_0 ∂_x Φ

instead of

∂_x Φ

as the Governing equations say. I didn't know which of the two is correct so I left them as is.

NOTE 2

The notation δ_k in ALE algorithm is never defined.

[adcroft]

Indeed, grad Phi should be multiplied by rho/rho_0.

[navidcy]

@adcroft have a look now.

1. What is the definition of \delta_k in ALE?

2. I'm a bit confused with the horizontal gradient of the geopotential Φ. If Φ=gz, then in the continuous version of the equations (before averaging over layer thicknesses) isn't the term ∂_x Φ = ∂_y Φ = 0? Why does it then appear in governing.rst?