Update deprecated syntax and fix vignettes

[andrjohns]

The Stan code used in the examples & vignettes (and some of the demonstrative c++) has since been deprecated or removed. Additionally, the vignettes were failing to build due to some configuration/compilation issues.

The following changes have been made in this PR:

• Stan syntax used in the rstan examples and vignettes updated to remove any deprecated syntax
• StanHeaders was not compiling sundials/sundials_context.c under unix, leading to ODE linking errors in the vignette
• StanHeaders::stanFunction() was not using the package's CXXFLAGS, leading to compilation errors due to the missing -D_REENTRANT under unix when building the vignette
• The rstan external c++ vignette was using stan::math::precomp_v_vari() which has since been removed

[andrjohns]

Note that the diff is a little inflated due to my IDE stripping trailing whitespace, you can see the diff with those filtered out here: https://github.com/stan-dev/rstan/pull/1055/files?w=1

[andrjohns]

Obsolete