ouch, those comments hurt my eyes! consider using the __END__ marker and you can follow with all the free text you want.

# Lines 4 and 5 are good Perl practice.  "strict" and "warnings" are p
+ragmas
# that help prevent Perl programmers from doing silly things in their 
+programs.
#
[download]

becomes

__END__
Lines 4 and 5 are good Perl practice.  "strict" and "warnings" are pra
+gmas
that help prevent Perl programmers from doing silly things in their pr
+ograms.

<code>

<p>also, you might consider using here documents rather than multiple 
+print statements.</p>

<code>
print OUT "For unique files in OldInventory.txt:\n";
print OUT "IGNORING FILES WITH Tmp OR Temp IN PATHNAME.\n";
print OUT "IGNORING FILES IN THE RECYCLE BIN.\n";
print OUT "IGNORING ALL HISTORY FILES.\n";
print OUT "LOWERCASING ALL FILE AND PATHNAMES BEFORE COMPARING.\n";
print OUT "\n";
[download]

becomes clearer, and more maintainable as

print OUT <<EOT;
For unique files in OldInventory.txt:
IGNORING FILES WITH Tmp OR Temp IN PATHNAME.
IGNORING FILES IN THE RECYCLE BIN.
IGNORING ALL HISTORY FILES.
LOWERCASING ALL FILE AND PATHNAMES BEFORE COMPARING.

EOT
[download]

it's one more useful concept to teach a user, and not difficult to understand.