Use the prompt() method from ExtUtils::MakeMaker/Module::Build.

Move your *.pm files in a directory named 'lib'. The directory structure should look like 'lib/Your/Module.pm' for a module named 'Your::Module'. If you need to provide additional files, e.g. for testing, that should not be considered for Kwalitee, then you should look at the 'provides' map in META.yml to limit the files scanned; or use the 'no_index' map to exclude parts of the distribution.

Error: CryptFile/lib/Filter/Crypto/CryptFile.pm, Decrypt/lib/Filter/Crypto/Decrypt.pm

Add all modules contained in this distribution to the META.yml field 'provides'. Module::Build or Dist::Zilla::Plugin::MetaProvides do this automatically for you.