Files and directory comparison with md5deep matching mode (see http://md5deep.sourceforge.net/start-md5deep.html#match).

md5deep.sh

# Create a reference folder with some data
mkdir foo
echo "hey" > foo/A.txt
echo "scm" > foo/B.txt
echo "git" > foo/C.txt

# Generate the list of hashes for each file
# -b = bare mode (strips any leading directory
#      information from displayed filenames)
md5deep -b foo/* > hashes.txt

# Create a modified folder with some changes
# A.txt: modified
# C.txt: deleted
# D.txt: added
mkdir bar
echo "HEY" > bar/A.txt
echo "scm" > bar/B.txt
echo "svn" > bar/D.txt

# Find the positive matches with the -m option
# ~ find all unmodified files
md5deep -bm hashes.txt bar/*
# => B.txt

# Find the negative matches with the -x option
# ~ find all added or modified files
md5deep -bx hashes.txt bar/*
# => A.txt
# => D.txt