It is said that the best debugging aid is a set of liberally sprinkled print statements and some careful logical thought.

I find it useful to give most of my larger programs a 'verbose' mode which prints out progress indication, time spent, contents of data structures and whatnot. The easiest way of doing so is to have a sub:

sub debug_info {
  print join ':', "\n*", @_;
  print "\n";
  return 1;
}
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then throughout the program have lines like:

debug_info('plotting world domination',$foo, $bar) if $verbose;

I usually make a command line option for verbosity with something like:

my $verbose = $ARGV[0] || 0;