If you want to re-define a subroutine in a module to suit your needs, consider either creating a descendant class or use eval to re-define the subroutine:

package MyClass2;
use MyClass;
use Exporter;
@ISA = ('MyClass');
@EXPORT = @MyClass2::EXPORT;

sub overridden {
   print "This is *my* method, overriding MyClass::overridden!\n";
}
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Or:

#!/usr/bin/perl

use MyClass;

sub MyClass::overridden {
   print "I need this to behave differently.\n";
}
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Or:

#!/usr/bin/perl

use MyClass;

my $code = get_some_code_text;

eval "sub MyClass::overridden { $code }";
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Using eval in this way lets you completely re-define your functions internally, even stuff in other modules, without needing to write your changes in a new file and then "re-use" (re-execute) that file to get your changes to take effect. Persistency might be a good reason to want to edit the source directly, though, so I understand that.