Shape up of docs and a litte reorganization

Removing unused files

Remove -optimize to fix doc target...

... this feels like a reasonable compromize.

Improved documentation of extensions

General improvments of the setup docs

Moving SetupFileCreator into apps package

Moving the report parser into apps

Better documentation of Apps

Documentation of the SetupReaderAPI.

Alignment documents and single read ...

... instead of single strand for tophat case class.

More docs of the Utils

Docs for Picard extensions

Fixing annotation typos

Adding package files
Merge branch 'devel' of github.com:johandahlberg/piper into devel