Add protocol prompt area before history

Introduce a new prompt "protocol" separate from extras: add LoopData.protocol_temporary and protocol_persistent, include protocol contents before message history during prompt construction, and clear temporary protocol data each turn. Add helper _build_context_message to render protocol/extras, update response input conversion to include protocol, and move project instructions & active/loaded skills injection into protocol. Update docs, prompts, plugin metadata, the SkillsTool message, and add tests to verify protocol placement and behavior.

extensions/python/AGENTS.md

@@ -44,7 +44,7 @@ Direct child DOX files:
 | [hist_add_tool_result/AGENTS.md](hist_add_tool_result/AGENTS.md) | Tool-result history side effects. |
 | [job_loop/AGENTS.md](job_loop/AGENTS.md) | Periodic backend maintenance jobs. |
 | [message_loop_end/AGENTS.md](message_loop_end/AGENTS.md) | End-of-message-loop history and persistence behavior. |
-| [message_loop_prompts_after/AGENTS.md](message_loop_prompts_after/AGENTS.md) | Prompt extras appended after message-loop prompt construction. |
+| [message_loop_prompts_after/AGENTS.md](message_loop_prompts_after/AGENTS.md) | Prompt protocol and extras assembled around message-loop prompt construction. |
 | [message_loop_prompts_before/AGENTS.md](message_loop_prompts_before/AGENTS.md) | Pre-prompt-construction message-loop gates. |
 | [message_loop_start/AGENTS.md](message_loop_start/AGENTS.md) | Start-of-message-loop iteration state. |
 | [monologue_end/AGENTS.md](monologue_end/AGENTS.md) | End-of-monologue UI and cleanup behavior. |

extensions/python/message_loop_prompts_after/AGENTS.md

@@ -2,11 +2,12 @@
 
 ## Purpose
 
-- Own prompt extras appended after primary message-loop prompt construction.
+- Own prompt protocol and extras appended around primary message-loop prompt construction.
 
 ## Ownership
 
 - Ordered Python files own current datetime, skill recall/load context, agent info, parallel job status, and workdir extras injection.
+- Loaded and active skill instructions belong in prompt protocol, not prompt extras.
 
 ## Local Contracts
 
@@ -16,11 +17,11 @@
 
 ## Work Guidance
 
-- Coordinate prompt-extra changes with skill, workdir, and profile contracts.
+- Coordinate prompt protocol and prompt-extra changes with skill, workdir, and profile contracts.
 
 ## Verification
 
-- Inspect rendered prompt extras or run prompt-construction tests after changes.
+- Inspect rendered prompt protocol/extras or run prompt-construction tests after changes.
 
 ## Child DOX Index
 

extensions/python/message_loop_prompts_after/_65_include_loaded_skills.py

@@ -9,7 +9,8 @@ class IncludeLoadedSkills(Extension):
         if not self.agent:
             return
 
-        extras = loop_data.extras_persistent
+        protocol = loop_data.protocol_persistent
+        protocol.pop("loaded_skills", None)
 
         # Get loaded skills names
         skill_names = self.agent.data.get(DATA_NAME_LOADED_SKILLS)
@@ -31,8 +32,8 @@ class IncludeLoadedSkills(Extension):
             return
 
 
-        # Inject into extras
-        extras["loaded_skills"] = self.agent.read_prompt(
+        # Inject into protocol
+        protocol["loaded_skills"] = self.agent.read_prompt(
             "agent.system.skills.loaded.md",
             skills=content,
         )

extensions/python/system_prompt/AGENTS.md

@@ -7,6 +7,7 @@
 ## Ownership
 
 - Ordered Python files own main, tools, MCP, secrets, skills, and project prompt sections.
+- Active project instruction bodies are moved into prompt protocol; the system prompt keeps project metadata and stable project rules.
 
 ## Local Contracts
 

extensions/python/system_prompt/_14_project_prompt.py

@@ -15,17 +15,24 @@ class ProjectPrompt(Extension):
     ):
         if not self.agent:
             return
-        prompt = await build_prompt(self.agent)
+        prompt = await build_prompt(self.agent, loop_data=loop_data)
         if prompt:
             system_prompt.append(prompt)
 
 
 @extensible
-async def build_prompt(agent: Agent) -> str:
+async def build_prompt(agent: Agent, loop_data: LoopData | None = None) -> str:
     result = agent.read_prompt("agent.system.projects.main.md")
     project_name = agent.context.get_data(projects.CONTEXT_DATA_KEY_PROJECT)
+    if loop_data:
+        loop_data.protocol_persistent.pop("project_instructions", None)
     if project_name:
         project_vars = projects.build_system_prompt_vars(project_name)
+        if loop_data and project_vars.get("project_instructions"):
+            loop_data.protocol_persistent["project_instructions"] = agent.read_prompt(
+                "agent.protocol.projects.instructions.md",
+                **project_vars,
+            )
         result += "\n\n" + agent.read_prompt(
             "agent.system.projects.active.md", **project_vars
         )