Add Filter dependancy to Input package

composer.json was missing the require for joomla/filter.
Change Input\Input to take a copy of _REQUEST, not a reference.

Input needs to be decoupled from altering _REQUEST.
Updated docs to namespacing format (closes #53).
Fix Input unit tests.
Make Application\Base logger aware.

Logging in an application is a fairly typical requirement so the
Application\Base class has been made PSR-3 logger aware.

Also added is an `initialise` method for developers to override.

Docs are added to cover these two things.
Adding basic initialisation example and logging notes to Database package README
Refactor logging out of Daemon.

Remove the logging out of Daemon (now in Base).
Add a `hasLogger` method for optional logger handling.
Update the README.
Remove the getInstance() method from Joomla\Filter\Input.
Use a closure in Joomla\Filter\Output::linkXHTMLSafe() to avoid an internal method in the class signature.
Move the routers into their own package.