Turns out that to copy a complete directory structure gulp
needs to be provided with a base for your gulp.src()
method.
So gulp.src( [ files ], { "base" : "." })
can be used in the structure above to copy all the directories recursively.
If, like me, you may forget this then try:
gulp.copy=function(src,dest){
return gulp.src(src, {base:"."})
.pipe(gulp.dest(dest));
};