Parameters can now be optional or required, which allows for more advanced template usage.
Updated existing templates to set the required flag.
Added documentation for root level analyses apis via existing templates.

This includes mention of literal style folding, field ordering, descriptions in JSON schemas.

Coverage report is generated by running integration tests, and
coverage can be checked by running `grunt coverage`.

Lint errors will now break the build.

Also reduces number of lint false positives.

This is done by reducing duplication of template arguments, and
formalized $include/$template into the flattenSwagger step.

Added documentation for collections.

This is a naive implementation of resolving JSON schema links,
will want to pull schemas into definitions eventually.