As others have said, use a hash rather than symbolic references. Here's how:

#! perl -slw
use strict;
use Data::Dump qw[ pp ];

my %cmds;

for my $fname ( <*Cmd.pm> ) {
    print $fname;
    my( $name ) = $fname =~ m[(^.+)Cmd.pm];
    %{ $cmds{ $name } } = do $fname;
}

pp \%cmds;

__END__
C:\test>832090.pl
billCmd.pm
fredCmd.pm
{
  bill => {
        command_1 => {
               Command_maps  => [],
               _discussion   => "\n       some text about command_1",
               build_types   => ["FLIGHT"],
               cmd_id        => 250033,
               constraints   => undef,
               description   => "\n       shorter text about command_1
+",
               fixed_pattern => 143,
               safety_level  => "SAFE",
               target        => "command_target",
             },
        command_2 => {
               Command_maps  => [],
               _discussion   => "\n       some text about command_2",
               build_types   => ["FLIGHT"],
               cmd_id        => 250014,
               constraints   => undef,
               description   => "\n       shorter text about command_2
+",
               fixed_pattern => 144,
               safety_level  => "SAFE",
               target        => "command_target",
             },
      },
  fred => {
        command_1 => {
               Command_maps  => [],
               _discussion   => "\n       some text about command_1",
               build_types   => ["FLIGHT"],
               cmd_id        => 250033,
               constraints   => undef,
               description   => "\n       shorter text about command_1
+",
               fixed_pattern => 143,
               safety_level  => "SAFE",
               target        => "command_target",
             },
        command_2 => {
               Command_maps  => [],
               _discussion   => "\n       some text about command_2",
               build_types   => ["FLIGHT"],
               cmd_id        => 250014,
               constraints   => undef,
               description   => "\n       shorter text about command_2
+",
               fixed_pattern => 144,
               safety_level  => "SAFE",
               target        => "command_target",
             },
      },
}
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