FIX: Adjustments for main branch to compile

[mmcky]

Make some adjustments to fix:

1. headers
2. equation references
3. execution for ar1_turningpts

[mmcky]

@thomassargent30 in prob_matrix there is the following text

TOM -- REWRITE OR MAYBE DROP PARTS OF 

[mmcky]

@thomassargent30 latex doesn't appear to like this math equation

$$
Z_t(Y(\omega)) := \left\{ 
\begin{array} {c}
\ 1 & \text{if } Y_t(\omega)< Y_{t-1}(\omega)< Y_{t-2}(\omega) \geq Y_{t-3}(\omega) \\
0 & \text{otherwise}
\end{array} \right.
$$

Can we use align instead?

It looks like the offending Tex is 516d0c1

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