about readability:

• please consider using perltidy to reformat your code, it solves most problems afoken mentioned
• use blank lines between logical steps, see commenting in chunks in Perl Best Practices
• take care about naming conventions and clarity
  hasref seems to mean hash_ref but reads like a boolean has_a_reference
• avoid deeply nested code!
  e.g. using a dispatcher like $cmd{$line}->() with %cmd=('**'=>\&dump_readme,'*'=>...)
• prefer self commenting code, like moving code chunks into well named subs

about commenting

• be sure which audience you are targeting whith your comments
• you seem to mix POD stuff (i.e. for the user) and dev-comments and (sorry) banalities,
• line quantity doesn't equal quality

about techniques:

• your begin block is huge and I'm puzzled why (?) ¹
• your repeatedly looping with $_ over most of your lines, that's very vulnerable to bugs
• &sub() in Perl5 is usable in the rare cases where you need to ignore prototypes

In general I'm sure you would love to have a look into Damian's PBP book.

This book helped me a lot understanding the traps in Perl and I hope it'll help you too! :)

Updates

¹) if you need to check UserAgent within BEGIN, I'd consider using a second BEGIN block

2) I.e. the top-down structure is hidden