[3.0] Move to a configuration file

[shalvah]

I've noticed a couple of PRs adding more and more command-line options. Currently, there are 13 command-line options. I'm thinking it would be better to move to a config file to make things cleaner.

[shalvah]

We can define a config file which the user can publish, say config/apidoc.php. By default, the package will use settings from the config file, but individual options can be overriden by specifying a command-line argument,

This would especially be helpful for teams which want to add a one-line composer script to generate docs.