Clean up the documentation in several places

[xylar]

• Reorganize the documentation to be more like compass
• Exclude the template from the design documents in the documentation
• Make the path to AnalysisTask simpler in the API (which makes is easier to reference elsewhere in the docs)
• Add missing API for several methods of RemapMpasClimatologySubtask
• Fix incorrectly formatted docstrings in RemapMpasClimatologySubtask

[xylar]

Testing

I build the documentation locally with this branch and it looks fine (though it's hard to be 100% sure with so many changes) and builds without errors.