Lets run those command on the machines

New instanceOld instance
find / -xdev | sort > new.txt find / -xdev | sort > old.txt

Pull the files locally

scp -i ~/.ssh/somekey ec2-user@  /tmp/new.txt
scp -i ~/.ssh/somekey ec2-user@  /tmp/old.txt

Then use this great delta tool to compare the files

delta -s /tmp/new.txt /tmp/old.txt

Using md5 sums

And a using md5 sums – this is slow!

# On the new instance

find / -xdev -type f -exec  md5sum {} \; > new-files.txt
find / -xdev -type d | sort > sorted.new-folders.txt
sort  -k2  new-files >sorted.new-files.txt 

# On the old instance

find / -xdev -type f -exec  md5sum {} \; > old-files.txt
find / -xdev -type d | sort > sorted.old-folders.txt
sort  -k2  old-files >sorted.old-files.txt