Clean up CLI option processing

[kutis96]

The current way is a bit messy:

• Each "module" has its own CLI processing
• The first arg is always the module name
• No way to add common options to all modules
• Aaaa.

Cleanup

• Create new Main classes for each of the modules, default to using the MarkdownModule
  • If anyone wants to use other modules as a main, they can do that in the usual Java ways for now. It's not like there are any users these days anyway. :')
• Remove the module multiplexing stuff for now
• Figure out some way of extracting common functionality (like config property loading) from the command processor so it can be shared, just in case one was to add the multi-module stuff later