Update docs with new subworkflows

[jonasscheid]

The documentation needs a bit of an overhaul due to the introduction of global fdr-mode and the the spectrum library generation subworkflow. The rescoring subworkflow has been introduced as well (without changes to the implementation logic)

Also #381

Edit: After discussion with @axelwalter, it would be need to have multiple explanatory figures in the README that explain the major concepts of the pipeline.