Part 3: cleanup of collection input/output now in core

[fmigneault]

Applies a much needed cleanup of Part 3: Workflows and Chaining.

• Remove "collections" requirement classes since they are now moved in Part 1: Core
• Updates a few updated references and improve cross-references between standards within requirements
• Define missing terms and use them (and align across parts in a consistent format)
• Switch HTTP to HTTPS for requirements and document references

I left the input/output field modifiers since, although partially covered in Core, there are a few patterns (notably properties) that are employed beyond collections, which is only what Core covers.

Updates related to CWL are defined into:

• Part 3: proposal for functional CWL ad-hoc execution with multipart #607

They should technically merge nicely, but a second pass of extra terms/cross-refs could be needed.

FYI @pvretano @jerstlouis