Document all stan code

[jamesmbaazam]

The stan code here has very little documentation, so there is a need to make this a priority to improve navigation. This can be done with Doxygen as mentioned here epinowcast/epinowcast#423.

[seabbs]

In a similar vein there are many easy to close test gaps in the stan code.

[seabbs]

Doxygen docs are also in https://primarycensored.epinowcast.org/stan/primarycensored_8stan.html thanks to @jamesmbaazam (though could really do with another pass to make the site easier to explore) and that package now gives a model of how to do this