rsync and md5sum: Use rsync to copy a directory and then generate a file containing the md5sum of all the files in source directory. Finally do a check of the md5sum of the target.

cpmd5.sh

#!/bin/bash
if [ $# -lt 2 ]; then
   echo "Usage: $0 source dest [md5file]"
   echo "Copy source directory into dest directory and put md5 sum of the files in source in md5file. "
   echo "If no md5 file is unspecified it is created in current directory"
   echo
   exit 0
fi
source=$1
target=$2
if [ $# -gt 2 ]; then
    md5file=$3
else
    md5file="`pwd`/`basename \"$source\"`.md5"
fi

# Remove trailing slash - we don't want that behavior of rsync
end=$((${#source}-1))
echo "END $end"
echo "${source:$end:1}"
if [ "${source:$end:1}" = / ]; then
    source="${source:0:$end}"    
fi
echo "Copying ${source} to ${target}"
rsync -avz --chmod=ugo=rwX "${source}" "${target}"
pushd "$source"
# add the copied dirname to target path
tmp=$(basename "$source")
target="$target/$tmp"

index=0
tmp=$md5file
while [ -f "$tmp" ]; do
    echo "File $tmp already exists."
    tmp="$md5file.$index"
    index=$[$index+1]
done

# This solves problem with spaces in dir name:
# http://stackoverflow.com/questions/7194192/basename-with-spaces-in-a-bash-script
fbase=$(basename "$tmp")
echo "Basename of md5file: $fbase"
# In case the md5filename has no directory part specified put it in
# target directory
if [ "$fbase" = "$tmp" ]; then
    tmp="$target/$tmp"
    echo "Md5target: $tmp"
else
    echo "Md5target1: $tmp"    
fi

echo "Calculating md5sum and saving in $tmp."
find . -type f -exec md5sum {} \; > "$tmp"

if [ "${tmp:0:1}" = / ]; then
    md5file="$tmp"
else
    md5file=$(pwd)/$tmp
fi
echo "Original $tmp, realpath $md5file"
# if [[ "${source:$end:1}" != / ]]; then
echo "Target dir $target"
# fi
popd
echo "Dumped md5sum in $tmp"
pushd "$target"
echo "Checking md5sum for copied files: $md5file"
md5sum -c "$md5file"
cp "$md5file" ./
popd