my %hash;

while (<>) {
  chomp;
  my ($key, $val) = split(/=/, $_, 2);
  my @elts = split(/\./, $key);

  my $p = \\%hash;
  $p = \( ${$p}->{$_} ) for @elts;

  $$p = $val;
}

use Data::Dumper;
print Dumper(\%hash);