Okay, here is one way to populate the hash:

#!/usr/bin/perl -w
use strict;

my %hash;
while( <> ) {
    chomp $_;
    my @trib= grep { "" ne $_ } split /(...)/, $_;
    my $ref= \\%hash;
    while(  @trib  ) {
        $ref= \$$ref->{shift @trib};
    }
    $$ref++;
}
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Note how I avoided having to save shift @trib to index into the next subhash by keeping a reference to the slot for the hash value instead of a reference to the hash.

If that code makes sense to you right away, then you are either sick, overlooking something, or do way too much work with Perl references. (:

P.S. I was seriously disappointed that

    my @trib= split /(?<=\G...)/, $_;
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