So I'm determined to do it the hard way, so that at the end (if there is an end),

Doing it the hard way is a time-honored tradition :) I just suggested you check out how the others work so that you can steal good ideas & interfaces.

is the long string in your penultimate line a single scalar for all purposes?

You mean $character{'Bob the Fighter'}->{'Attributes'}->{'Str'}? Yes, because in the end it is just a value stored in a hash, and only scalars can be thus stored. By dereferencing part of that mess, you can get a hash. For example, %{ $character{'Bob the Fighter'}->{'Attributes'} } is the Attributes hash. (The scalar value $characters{'Bob the Fighter'}->{'Attributes'} is a reference to a hash. the %{ } dereferences the reference.

Could I include lists in that hash by reference?

Absolutely. A reference to anything is a scalar, and a hash can store a scalar. An anonymous list can be created by [], or you can use the backslash reference. So:

$characters{'Bob the Fighter'}->{'Feats'}= [ 'Strong Spit', 'Perl Guru
+'];
# or
@feats = ('Strong Spit', 'Perl Guru');
$characters{'Bob the Fighter'}->{'Feats'} = \@feats;
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both work just fine. You can then access them like:

$characters{'Bob the Fighter'}->{'Feats'}->[1];
#is equal to 'Perl Guru'
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Remember that although we're using a hash as our "base" variable here, we could use any other data type that is appropriate. A list could work:

$characters[3]->{'Attributes'}->{'Str'};
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as could a scalar:

$characters->{'Bob the Fighter'}->{'Attributes'}->{'Str'};
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(Assuming you had stored the data in that fashion.)

If, for example, $character{'Bob'}->{'Class'} holds 'Ftr', and $class{'Ftr'}->{'Base Attack'} holds 'Good' (to indicate that fighters have Good attack bonuses, which are generated by a short procedure in the combat module), what would be the code to retrieve Bob's Base Attack type?

Well, $class{$character{'Bob'}->{'class'}}->{'Base Attack'} would be equal to $class{'Ftr'->{'Base Attack'} (actually, it would _BE_ the same, since all that happens is $character{'Bob'}->{'Class'} resolves to 'Ftr') However, this assumes that Bob's class will ALWAYS have an entry in %class.

Storing feats, spells, etc. as booleans is not efficient, IMHO. I want to be able to brew a new feat and not have to go and set the bit in all the PCs.)

Just so you know, Perl handles non-existant hash keys quite nicely, and it's quite common to see code that would be like:

if($char{Bob}->{Feats}->{'Good With Pointy Objects'}){
    Kill_Bad_Guy();
} else {
    Die_Hideous_Death();
}
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If Bob doesn't have that feat, you don't have to set it to 0, you simply don't set it to a true value, and it will evaluate False. (Well, undefined, which in turn is false)