36 # get a timestamp in the format YYYYMMDDHMS
     37 my ($year, $month, $dayofmonth, $hour, $minute, $second)
     38         = (localtime())[5, 4, 3, 2, 1, 0];
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Why not just assign the variables in the order that localtime returns them:

# get a timestamp in the format YYYYMMDDHMS
my ( $second, $minute, $hour, $dayofmonth, $month, $year )
        = localtime;
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     70 parse_config($path_to_conf_file) if $path_to_conf_file;

    100 # declare LOG file handle
    101 my $LOG;
    102 sysopen ($LOG, $path_to_log_file, O_WRONLY | O_APPEND | O_CREA
+T)
    103     or die "Can't open $path_to_log_file: $!";
    104 # We'll try and keep a lock on the log file for the duration o
+f our script
    105 flock($LOG, LOCK_EX)        or die "Can't get a lock on $path_
+to_log_file";

    201         if (/^log-file\s*=\s*(.+)$/) {
    202             if (-d $1) {
    203                 warn "in $conf_filename line $.: $1 is a direc
+tory";
    204                 next;
    205             }
    206             unless (-e $1) {
    207                 unless (open(LOG, ">", $1)) {
    208                     warn "in $conf_filename line $.: Cannot op
+en $1 for writing: $!";
    209                     next;
    210                 }
    211                 print LOG "[" . scalar(localtime()) . "] Creat
+ed logfile\n";
    212             }
    213             close(LOG);
    214             $path_to_log_file = $1;
    215             next;
    216         }
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You call parse_config() on line 70 which opens and prints to and closes the log file and then sets the variable $path_to_log_file which is subsequently used to open the log file again.   Do you really need to open the log file inside the parse_config() function?

    268 sub logger {
    269     my ($message, $level) = @_;
    270     return if $level > $log_level;
    271     
    272     # name log levels
    273     my @level_names = qw( NONE ERROR WARNING INFO DEBUG );
    274     
    275     # autoflush output for current scope only
    276     local $| = 1;
    277     
    278     # DEBUG
    279     #print "\@level_names:\n";
    280     #print "\t$_\n" foreach @level_names;
    281     #print "\$level: $level\n";
    282     #print "\$message: $message\n";
    283     
    284     print $LOG "[" . scalar(localtime()) . "] " . $level_names
+[$level] . ": $message\n";
    285 }
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You are changing the value of the $| variable which turns on autoflush for the currently selected file handle which by default is STDOUT so it will have no effect on the following print statement.   Since you are opening the log file with sysopen perhaps you should write the log message using syswrite which bypasses buffered IO.

    syswrite $LOG "[" . scalar(localtime()) . "] " . $level_names[$lev
+el] . ": $message\n";
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    202             if (-d $1) {
    203                 warn "in $conf_filename line $.: $1 is a direc
+tory";
    204                 next;
    205             }
    206             unless (-e $1) {

    218             if (-d $1) {
    219                 warn "in $conf_filename line $.: $1 is a direc
+tory";
    220                 next;
    221             }
    222             unless (-e $1) {
[download]

To avoid stating the same file twice you can use the special _ filehandle:

    202             if (-d $1) {
    203                 warn "in $conf_filename line $.: $1 is a direc
+tory";
    204                 next;
    205             }
    206             unless (-e _) {

    218             if (-d $1) {
    219                 warn "in $conf_filename line $.: $1 is a direc
+tory";
    220                 next;
    221             }
    222             unless (-e _) {
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