A Protocol is any kind of agreement on meaning between two parties. For example, suppose a server vends popular music, but under an ASCAP license that requires copyright disclosure. The protocol required between the two parties is ``copyright-disclosure'' which requires the joint presentation of an audio resource and a text resource.
How that is done should be outside the specification. Whether one particular system views the protocol request as an RPC command to flash some text on the screen, or another chooses to display an HTML page, or yet another chooses to include a synthesized rendering after the song, is an implementation detail.
In that spirit, the Protocols presented here are agreements about messages, pre/postconditions, and semantics, but not about software architecture.
While we may often refer to ``constructing a pipeline'' or ``the decryption stage of a pipeline,'' each Protocol must stand alone as an agreement on the message between two parties.