Initial refactoring to a single middleware based pipeline

Minor tweak
Created `TurtleIO.routes()` to return middleware routes & refactored `TurtleIO.run()` & `TurtleIO.allowed()` to utilize it, removed historical, removing useless tests
Differentiating between a 404 & 405 when `catchAll` is active

Fixing a test

Tweaks

Fixing checks

Updating docs

Fixing a typo
Adding `TurtleIO.routeCache` to minimize redundant list building, invalidating when `catchAll` triggers `TurteIO.handle()`
Major version change to reflect new `module.exports` factory

Fixing alignment
Decorating `TurtleIO` instance as `req.server`
Merge pull request #307 from avoidwork/BetterPipeline

Better pipeline