Move script to real location
Remove default locations for modules and output

They make no sense for general use so remove them and make sensible errors happen.
Also remove anachronistic line wrapping.
Encode paths in code tags

This should make things like /software/tags look better.
Change default filename for index

index.md seems right
Use documentation layout
Specify subcategory and menu for documentation layout
Change toplogy of output files

* Remove ncm- prefix from components.
* Make each document an index of a subdirectory.
* Add subdirectories for subclasses.
* Write a menu document relative to the main location
* Make menu list generation optional and configurable