Then, use the UNIX command diff to compare the two directories. This will show the differences in the directories. You can use diff -r dir1 dir2 two recurse and show the differences in text files in each directory(.xml, .properties, etc).
#Extract the jar (war or ear)
cd dir1
jar xvf jar-file1
for i in `ls *.class`
do
javap $i > ${i}.txt #list the functions/variables etc
done
cd dir2
jar xvf jar-file2
for i in `ls *.class`
do
javap $i > ${i}.txt #list the functions/variables etc
done
diff -r dir1 dir2 #diff recursively