I completely agree with @sakrejda here. Shipping additional scripts that aren't well-tested with different boundary conditions will just add to the maintenance burden and confusion. If anyone can actually write scripts that will work (and really list the conditions under which it won't), we can distribute those.
@bhomass, here's how a Stan program is compiled on my Mac using clang++:
clang++ -I src -I stan/src -isystem stan/lib/stan_math/ -isystem stan/lib/stan_math/lib/eigen_3.3.3 -isystem stan/lib/stan_math/lib/boost_1.62.0 -isystem stan/lib/stan_math/lib/cvodes_2.9.0/include -Wall -DEIGEN_NO_DEBUG -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DFUSION_MAX_VECTOR_SIZE=12 -DNO_FPRINTF_OUTPUT -pipe -Wno-unused-function -ftemplate-depth-256 -O3 -o examples/bernoulli/bernoulli src/cmdstan/main.cpp -include examples/bernoulli/bernoulli.hpp stan/lib/stan_math/lib/cvodes_2.9.0/lib/libsundials_nvecserial.a stan/lib/stan_math/lib/cvodes_2.9.0/lib/libsundials_cvodes.a
The C++ compilers that we work with (clang++, g++) don't have issues with spaces, so you can adjust that line to have it compile from an arbitrary directory. All you would have to do is change paths for all the includes and the input and output filenames.