Any ideas on how I can avoid 4000 lines of many module subs in one source file?

Um ... put package Mod; at the top of each of Mod-part1.pm and Mod-part2.pm?

The package statement doesn't propagate beyond file boundaries so you need to be explicit in your individual files

Update: Sorry, I didn't see what you had written about use base (that's what I get for skimming rather than reading). Hmm. You can always declare your subs like this:

sub Mod::foo { ... }
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And if variables are a problem too, then you would add

use vars qw($Mod::var1 $Mod::var2  @Mod::var3  %Mod::etc);
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at an appropriate place. Note that this still won't make __PACKAGE__ have the value of Mod

Why are you using __PACKAGE__ anyway? Do you need to? As chromatic said, perhaps you need to re-think your design.

Also, you can always redeclare everything at the top of each module part:

# Mod-part1.pm
package Mod;
use base qw(Meta);
...
# Mod-part2.pm
package Mod;
use base qw(Meta);
...
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