More Cleanups

* Remove docs/NewUserGuide.txt since I've put it in the wiki and it's not even distributed in .gem package. Not sure what to do about other doc/* files though.

* Remove some warnings found by `ruby -w` in thread-index-mode.rb

* Make chronic a hard dependency. The chronic gem is only 39k, written in pure ruby, has no .gem dependencies, works from 1.8.7 to 2.0.0. No reason not to include it as a hard dependency.

* Replace all `-` in filenames(mostly lib/sup/modes/*) with `_`. This is pretty much a convention in Ruby community. And we already have `_` in test files' names. I guess it's better to make this change before it's too late.