It would be good to see some oof your data, to try to figure out what you're doing and why.
Just a couple of comments on some code details, although it might be that it would be better to change it overall.
Why would you need this:
$s =~ s/^[ \t]+//mg; # remove leading whitespace from each line
$s =~ s/^\s+//; # remove leading whitespace
when the second line will do everything that the firstline is doing? (Same from trailing spaces).
Similarly, I don't see the reason to run the same pair of statements three times:
$s =~ s/^;.*\Z//m; chomp $s;
$s =~ s/^;.*\Z//m; chomp $s;
$s =~ s/^;.*\Z//m; chomp $s;
Once should be enough, no? And I doubt the
chomp is useful here.
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