While installing an R package containing Rcpp code using the devtools::install() command, two new folders - src-i386 and src-x64 were created. This would not happen earlier. Also this happens on a Windows system only. I'm guessing this is a result of a new feature added in the devtools package.
Question: Should these folders be included in the git repository?
No.
Only src/ should be included within a git repository.
The src-i386 and src-x64 folders are artifacts left over from a multi-architecture build on Windows (e.g. x86 and x64). These folders are the result of R's the command line install using R CMD INSTALL ..., which is wrapped by devtools.