Personally, I force all of my code to be in modules. For development I sometimes do actual perl code in my .pl scripts, but for the most part my scripts all look like

use My:Script:Foo;

My::Script::Foo->bar()
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This allows me to test all of my scripts by ensuring all of my modules are fully tested, and helps me organise my code by functional units instead of just throwing various and sundry subs into my scripts.