Added step to simplify swagger for code generation. Fixed a few missing types in schemas, added schemas for login/logout responses

Closes #1088

Removed packfile endpoints for sessions, collections, and acquisitions.
Added missing parameters to packfile and packfile-end endpoints.

Also refactored a few schemas to better match the SDK.

This documents the endpoints for /<container>/<cid>/analyses as well as
/<container>/<cid>/<subcontainer>/analyses.

This endpoint returns the JSON schema for gear configuration.

Added "session" query parameter that limits the returned acquisitions.

Added input schema for adding a job, and the endpoint for GET /job/{JobId}/logs.

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`.