This flattens the meta programs of the C++ stan math library

flatten_prim_meta.sh

# This script should do the following:

# 1) Move scal to prim/meta
# 2) Move mat to the prim/meta
#    a) if a file exists, just cat it to the end
#    b) properly handle the #ifndefs, and the brackets and stuff
# 3) Move arr
#    a) same logic as a) above
#    b) same logic as b) above
# we also need to creat the meta.hpp file properly



old_dir="/home/andre/cmdstan/stan/lib/stan_math/stan/math/prim"
new_dir="./stan/math/prim/"
#dims=("scal" "mat" "scal")


test="/home/andre/"
#ls -ltr "${old_dir}scal/meta/*"
#echo "$bew_"
#ls "$old_dir/scal/meta/"*

cp "$old_dir/scal/meta/"* "$new_dir/meta/"

# for file in "$new_dir/meta/"*;
# do
#     sed -i '/#endif/d' $file
#     head -n --lines=-2 $file > "$file.tmp"
#     mv "$file.tmp" $file
# done


for file in "$old_dir/mat/meta/"*;
do
    file_nm=${file##*/}
    if [ ! -f "$new_dir/meta/$file_nm" ]; ## check to see if that works
    then
        echo $file_nm
        # do we really need the git history for everything?
        cp "$file" "$new_dir/meta/"
    else
        # remove }*namespace and end if
        sed -i '/#endif/d' "$new_dir/meta/$file_nm"
        sed -i '/\/\/ namespace/d' "$new_dir/meta/$file_nm"
        
        sed '1,2d' $file > "$new_dir/meta/$file_nm.tmp1"
        cat "$new_dir/meta/$file_nm" "$new_dir/meta/$file_nm.tmp1" > "$new_dir/meta/$file_nm.tmp"
        mv "$new_dir/meta/$file_nm.tmp" "$new_dir/meta/$file_nm"
        rm "$new_dir/meta/$file_nm.tmp1"
        echo "catted"

        ## move includes to the top
        sed  '/#include/!H;//p;$!d;g;s/\n//' "$new_dir/meta/$file_nm" > "$new_dir/meta/$file_nm.tmp2"
        mv "$new_dir/meta/$file_nm.tmp2" "$new_dir/meta/$file_nm"

        ## move the #ifndef statements back to the top (lazy way to do it)
        sed  '/#define/!H;//p;$!d;g;s/\n//' "$new_dir/meta/$file_nm" > "$new_dir/meta/$file_nm.tmp3"
        mv "$new_dir/meta/$file_nm.tmp3" "$new_dir/meta/$file_nm"

        sed  '/#ifndef/!H;//p;$!d;g;s/\n//' "$new_dir/meta/$file_nm" > "$new_dir/meta/$file_nm.tmp4"
        mv "$new_dir/meta/$file_nm.tmp4" "$new_dir/meta/$file_nm"

        ## remove the second occurances of namespace stan and namespace math
        ## if line exists, remove all then re insert insert after includes
        if grep -q "namespace stan" "$new_dir/meta/$file_nm" ## if the file contains namespace stan
        then
            echo "asdfadsfa"
            sed -i '/namespace stan/d' "$new_dir/meta/$file_nm" ## delete lines containing namespace stan
            ## below: place after includes
            sed -i '1h;1!H;$!d;x;s/.*#include[^\n]*/&\nnamespace stan {/' "$new_dir/meta/$file_nm"
        fi

        ## now we do the same thing for math
        if grep -q "namespace math" "$new_dir/meta/$file_nm" ## if the file contains namespace math
        then
            echo "asdfadsfa"
            sed -i '/namespace math/d' "$new_dir/meta/$file_nm" ## delete lines containing namespace math
            ## below: place after includes
            sed -i '1h;1!H;$!d;x;s/.*#include[^\n]*/&\nnamespace math {/' "$new_dir/meta/$file_nm"
        fi
        
    fi
done

Instead of creating temp files, Andre, just use sed -i