structured-cp

#!/bin/bash

die()
{
    [ -n "$*" ] && echo "$@" >&2
    exit 1
}

target_base=$1
[ -n "$target_base" ] || die "Supply the directory to copy the thinned tree to"

while IFS= read -r file; do
    dir=${target_base}/${file%/*}
    mkdir -p "$dir" || die
    cp "$file" "$dir" || die
done