Very nice puzzle. Here is my solution:

use warnings;
use strict;

my @path;
my @data;
my $size = 0;
while(<DATA>) {
    chomp;
    $path[0]            = $1 if /^([^|]*)$/;
    $path[length($1)/3] = $2 if /^(.*\|--)([^-]+)$/;
    if( /^(.*\|--)-([^-]+)$/ ) {
        $#path = length($1)/3 - 1;
        push @data, [ @path, $2 ];
        $size = @path if $size < @path;
    }
}
splice @$_, -1, 0, ('')x(1+$size-@$_) for @data;
print join( "\t", @$_ ),"\n" for @data;

__DATA__
A
|
|--B
|  |
|  |--C
|     | 
|     |---PQR
|     |---XYZ
|--D
|  |
|  |---LMN
|---XYZ
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