#!/usr/bin/env perl

use strict;
use warnings;

use Data::Dump;

my (%data, $topkey);

while (<DATA>) {
    chomp;
    $data{$topkey}{$1} = $2 and next if /^(.*?)=(.*?)$/;
    $topkey = $_; 
}

dd \%data;

__DATA__
Paragraph1
key1=valueA
Paragraph2
key2=valueB
key3=valueC
Paragraph3

##</code><code>##

{
  Paragraph1 => { key1 => "valueA" },
  Paragraph2 => { key2 => "valueB", key3 => "valueC" },
}