Well, here's a best guess...

#!/usr/bin/perl

use strict; # https://perlmonks.org/?node_id=11136806
use warnings;

my %hash;
while( <DATA> )
  {
  chomp;
  my $code = s/\@/}{/gr;
  eval "\$hash{$code}++";
  }
#use Data::Dump 'dd'; dd \%hash;

sub nest
  {
  my $h = shift;
  my $answer = '';
  if( ref $h )
    {
    for my $k ( sort keys %$h )
      {
      $answer .= ref( $h->{$k} )
        ?  "$k {\n" . nest( $h->{$k} ) =~ s/^/\t/gmr . "}\n"
        : $k . "\n";
      }
    }
  $answer;
  }

local $_ = nest \%hash;
s/\w\K\n\s*(?=\w)/,/g;
print;

__DATA__
instreg@d1@d1
instreg@d1@d2
instreg@d2@d1
instreg@d3@d1
instreg@d4@d1
instreg@d5@d1
instreg@d6@d1
instreg@d7@d1
instreg@d8@d1
alureg@d1@d1
alureg@d2@d1
alureg@d3@d1
alureg@d4@d1
alureg@d5@d1
alureg@d6@d1
alureg@d7@d1
alureg@d8@d1
pgmctr@d1@d1
pgmctr@d2@d1
pgmctr@d3@d1
pgmctr@d4@d1
pgmctr@d5@d1
pgmctr@m1
pgmctr@m2
pgmctr@m3
pgmctr@m4
pgmctr@m5
[download]

Outputs:

alureg {
        d1 {
                d1
        }
        d2 {
                d1
        }
        d3 {
                d1
        }
        d4 {
                d1
        }
        d5 {
                d1
        }
        d6 {
                d1
        }
        d7 {
                d1
        }
        d8 {
                d1
        }
}
instreg {
        d1 {
                d1,d2
        }
        d2 {
                d1
        }
        d3 {
                d1
        }
        d4 {
                d1
        }
        d5 {
                d1
        }
        d6 {
                d1
        }
        d7 {
                d1
        }
        d8 {
                d1
        }
}
pgmctr {
        d1 {
                d1
        }
        d2 {
                d1
        }
        d3 {
                d1
        }
        d4 {
                d1
        }
        d5 {
                d1
        }
        m1,m2,m3,m4,m5
}
[download]

If this is not what you are looking for, please show the exact output you want, especially for pgmctr, which as LanX has pointed out, has an array/hash conflict.

P.S. This is also sure to upset the 'eval' haters :)

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