Fix LoosOptions pre-made command line options

[agrossfield]

---

name: Fix problems with the new LoosOptions module
about: Create a report to incorporate code
title: ''
labels: ''
assignees: ''

Fixes #71 and (partly) #72

Changes proposed in this pull request

- Changes the way fullhelps are handled in LoosOptions (#71)
- added descriptions to the tools that use LoosOptions (#71)
- started getting rid of required options, since that breaks help and fullhelp (partially address #72)