Standardize model-visible fragments

Fold Apps, Skills, and Plugins into the model-visible fragment registry as ordered developer-envelope fragments, keep the turn-state/contextual-user framework intact, and refresh prompt layout snapshots/docs around the new shape.

Co-authored-by: Codex <noreply@openai.com>

codex-rs/app-server-protocol/schema/json/v2/ThreadStartParams.json

@@ -145,6 +145,7 @@
       ]
     },
     "developerInstructions": {
+      "description": "Custom developer override for this thread session. Takes precedence over `~/.codex/config.toml` `developer_instructions`.",
       "type": [
         "string",
         "null"