Here's a breakdown of the code:

#!/usr/bin/perl -w
use strict;
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No explanation needed

$_="Perl in a box";
for(/\S/g){
@_=(@_=>lc)
}
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Put all of the characters from $_ into @_ in order after they've been lower cased, but no spaces.

my($i,$k)=(0,'');
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Variable decalaration

for(@_){
$_{$_}=$i++
}
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Sets up the magic decoder ring for the first level encoding. For each character in @_, set a value in %_ for the key corresponding to the character to the offset in @_. i.e. $_{p} = 0, $_{e} = 1, etc.

undef $/;
$_=<DATA>;
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Unset the input record separator and slurp in the encoded info in from DATA.

s;\s;;g;
for(/../g){
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After blowing away all whitespace in the encoded data, loop over the data 2 characters at a time.

my@k=/./g;
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Split the characters into @k.

@k=(pop@k,@k)if($k[1]ne lc$k[1]);
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Reverse the characters in the array if the second one is not lower case.

for my $k (@k){
$k=$_{lc$k};
}
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Decode the letters in @k with the magic decoder ring to get 2 numbers.

$k.=chr(30+pop(@k)+10*pop(@k));
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Multiply the first number in @k by 10, add 30 and the first number in @k, turn it into a character and add it onto the string $k, which is different than the $k we used in the for loop above.

}
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End the for(/../g) loop

$_=$k;
s|(.{20})|$1\n|g;
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Assign $k to $_ so the substitution looks better and do the substitution to turn $_ into 20 character long lines.

eval
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Eval the second obfuscated code. Wheew. Are we done yet? Nope. Here's what the second level decoder looks like:

$_=q[s;.*;94eae6e840
c2dcdee8d0cae440a0ca
e4                d8
40                d0
c2                c6
d6                ca
e4                14
;s                ;@
_=                /.
./                g;
fo                r(
@_                ){
$_                =c
hr                ((
he                x)
>>1)}$_=join'',@_;pr
int];s; |\n;;g;eval;
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In a slightly more readable form:

$_=q[
s;.*;94eae6e840c2dcdee8d0cae440a0cae4d840d0c2c6d6cae414;s;
@_=/../g;
for(@_){
    $_=chr((hex)>>1);
}
$_=join'',@_;
print
];
s; |\n;;g;
eval;
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This code simply sets up more code that loops through the encoded string (The 94eae6.... string that is put into $_ inside the quoted code to be evaled) 2 characters at a time, turns those characters into a real hex value, which in turn is shifted right 1 bit and turned into a character. After all of the characters have been decoded, they are crammed together and printed. A nice head-scratcher.