Update: For a more concrete application of the idea which is not as overdesigned as my approach, see kcott's reply.

I like the following cascade of options, but if you are just starting out with your program, I recommend that you go with the config file alone, or maybe config file + defaults. Here are the overkill steps to do that:

1. Set up defaults:

   sub get_defaults {
       return +{
         output_type => 'excel',
         output_dir  => '/tmp',
         ...
       };
   };
   [download]

2. Read a config file, maybe JSON or YAML. YAML is supposed to be "user-friendly" (which I think it isn't), but it's commonly used. JSON is a contender but it doesn't allow comments, which I think are important in a config file.

   use YAML 'LoadFile';
   
   sub config_from_file {
       my( $filename ) = @_;
       LoadFile( $filename )
   }
   [download]

3. Use switches from the environment:

   sub config_from_ENV {
       my ( $env ) = @_;
       {
           output_type => $env->{MYAPP_output_type},
           ...
       }
   }
   [download]

4. Use command line switches:

   sub config_from_ARGV {
       my( $argv ) = @_;
       GetOptionsFromArray (
           'f|config_file:s' => \my $config_file,
           't|output_type:s' => \my $output_type,
       );
       return +{
           config_file => $config_file,
           output_type => $output_type,
       },
   [download]

5. Merge all the values, starting from the default upwards:

   my $defaults = get_defaults();
   
   my $argv = config_from_ARGV( \@ARGV );
   my $config_file = $argv->{config_file} || 'myconfig.yml';
   my $file = config_from_file( $config_file );
   my $env  = config_from_ENV( \%ENV );
   
   # Merge the things
   my $final_config = $defaults;
   for my $cfg ($config_file, $env, $argv) {
       for my $entry (keys %$cfg) {
           if(defined $cfg->{$entry}) {
               $final_config->{ $entry } = $cfg->{ $entry };
           };
       };
   };
   [download]

6. Done

For a start, I would only implement get_defaults and config_from_ARGV, or even skip one of the two.

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