Yes. You just have to feed the appropriate file names to the fc command and look at what it gives you back. It so happened that I was comparing two shares to see where they differed, not quite the same as your problem ... but close enough.
I decided to do it the md5 way. So how would i accomplish this. I have it reading the directorys assign it to an array. Right now I am just printing the md5 hash from each element in the array. How would I assign each item to the array, and then loop though each array and compare each field?
my @rFileCheck = readdir(DIR);
my @lFileCheck = readdir(DIR);