Installation instructions blasts away user config without warning

[jbedo]

The readme currently instructs users to run:

fileConn<-file("~/.R/Makevars")
writeLines(c( "CXX14FLAGS += -O3","CXX14FLAGS += -DSTAN_THREADS", "CXX14FLAGS += -pthread"), fileConn)
close(fileConn)

This blasts away any config a user may already have configured at ~/.R/Makevars and is accompanied with no warnings. Users should be strongly warned that this will happen.

Moreover, the whole instruction could be avoided by detecting platforms and available compiler features in configure. Users would then not have to do anything special to configure the build environment.