feat(aia): Implement Protocol Agent MVP with reusable Agent framework

Sprint 1-3 Completed (Backend + Frontend):

Backend (Sprint 1-2):
- Implement 5-layer Agent framework (Query->Planner->Executor->Tools->Reflection)
- Create agent_schema with 6 tables (agent_definitions, stages, prompts, sessions, traces, reflexion_rules)
- Create protocol_schema with 2 tables (protocol_contexts, protocol_generations)
- Implement Protocol Agent core services (Orchestrator, ContextService, PromptBuilder)
- Integrate LLM service adapter (DeepSeek/Qwen/GPT-5/Claude)
- 6 API endpoints with full authentication
- 10/10 API tests passed

Frontend (Sprint 3):
- Add Protocol Agent entry in AgentHub (indigo theme card)
- Implement ProtocolAgentPage with 3-column layout
- Collapsible sidebar (Gemini style, 48px <-> 280px)
- StatePanel with 5 stage cards (scientific_question, pico, study_design, sample_size, endpoints)
- ChatArea with sync button and action cards integration
- 100% prototype design restoration (608 lines CSS)
- Detailed endpoints structure: baseline, exposure, outcomes, confounders

Features:
- 5-stage dialogue flow for research protocol design
- Conversation-driven interaction with sync-to-protocol button
- Real-time context state management
- One-click protocol generation button (UI ready, backend pending)

Database:
- agent_schema: 6 tables for reusable Agent framework
- protocol_schema: 2 tables for Protocol Agent
- Seed data: 1 agent + 5 stages + 9 prompts + 4 reflexion rules

Code Stats:
- Backend: 13 files, 4338 lines
- Frontend: 14 files, 2071 lines
- Total: 27 files, 6409 lines

Status: MVP core functionality completed, pending frontend-backend integration testing

Next: Sprint 4 - One-click protocol generation + Word export

backend/scripts/check-dc-tables.mjs

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backend/scripts/create-capability-schema.sql

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backend/scripts/create-tool-c-ai-history-table.mjs

@@ -216,6 +216,8 @@ createAiHistoryTable()
 
 
 
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backend/scripts/create-tool-c-table.js

@@ -203,6 +203,8 @@ createToolCTable()
 
 
 
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backend/scripts/create-tool-c-table.mjs

@@ -200,6 +200,8 @@ createToolCTable()
 
 
 
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backend/scripts/migrate-aia-prompts.ts

@@ -323,3 +323,5 @@ main()
 
 
 
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backend/scripts/setup-prompt-system.ts

@@ -128,5 +128,7 @@ main()
 
 
 
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backend/scripts/test-pkb-apis-simple.ts

@@ -347,6 +347,8 @@ runTests().catch(error => {
 
 
 
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backend/scripts/test-prompt-api.ts

@@ -94,5 +94,7 @@ testAPI().catch(console.error);
 
 
 
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backend/scripts/test-unifuncs-deepsearch.ts

@@ -126,3 +126,5 @@ testDeepSearch().catch(console.error);
 
 
 
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backend/scripts/verify-pkb-rvw-schema.ts

@@ -312,6 +312,8 @@ verifySchemas()
 
 
 
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