This isn't a very perlish answer, but have a look at rsync.

It's mainly used to synchronize between two hosts, but it has a '-n' flag that will just do the comparison. There's also a perl interface over here.

I find this quite handy, since it can compare 2 directory trees on the same host, or two directory trees on different hosts. A quick comparison that will look at ownership, group, ,permissions, modification times, sizes, checksums, etc, is as easy as:

rsync -nav /some/dir/ /other/dir/
[download]

The trailing slashes mean something, and don't forget the -n, or it will synchronize the two directories :)