Fix command line interface compatibility breakage

[theoreticalbts]

#3014 was unintentionally an incompatible change to the command-line interface. The problem here is that, in some places, the option needs to be separately added to the config and command line options. This cannot be done because here the plugin-specified options are added to both the config and command-line options.

So I propose the following refactoring:

• In every plugin's set_program_options(), have the common options for cli / cfg added to cfg as presently
• Add the line cli.add(cfg); to the plugin
• This is a pure refactoring, we've just moved the logic of "add everything in cfg to cli" from appbase to each individual plugin
• For every former bool_switch() option, after cli.add(cfg);, add bool_switch() to cli
• For every former bool_switch() option, after cli.add(cfg);, add value<bool> to cfg

[theoreticalbts]

#3024 will probably have to be reverted when this is implemented.