syndarix/docs/architecture/ARCHITECTURE_DEEP_ANALYSIS.md

# Syndarix Architecture Deep Analysis

**Version:** 1.0
**Date:** 2025-12-29
**Status:** Draft - Architectural Thinking

---

## Executive Summary

This document captures deep architectural thinking about Syndarix beyond the immediate spikes. It addresses complex challenges that arise when building a truly autonomous multi-agent system and proposes solutions based on first principles.

---

## 1. Agent Memory and Context Management

### The Challenge

Agents in Syndarix may work on projects for weeks or months. LLM context windows are finite (128K-200K tokens), but project context grows unboundedly. How do we maintain coherent agent "memory" over time?

### Analysis

**Context Window Constraints:**
| Model | Context Window | Practical Limit (with tools) |
|-------|---------------|------------------------------|
| Claude 3.5 Sonnet | 200K tokens | ~150K usable |
| GPT-4 Turbo | 128K tokens | ~100K usable |
| Llama 3 (70B) | 8K-128K tokens | ~80K usable |

**Memory Types Needed:**
1. **Working Memory** - Current task context (fits in context window)
2. **Short-term Memory** - Recent conversation history (RAG-retrievable)
3. **Long-term Memory** - Project knowledge, past decisions (RAG + summarization)
4. **Episodic Memory** - Specific past events/mistakes to learn from

### Proposed Architecture

```
┌─────────────────────────────────────────────────────────────────┐
│                     Agent Memory System                          │
├─────────────────────────────────────────────────────────────────┤
│                                                                  │
│  ┌──────────────┐   ┌──────────────┐   ┌──────────────┐        │
│  │   Working    │   │  Short-term  │   │  Long-term   │        │
│  │   Memory     │   │   Memory     │   │   Memory     │        │
│  │  (Context)   │   │   (Redis)    │   │  (pgvector)  │        │
│  └──────┬───────┘   └──────┬───────┘   └──────┬───────┘        │
│         │                   │                  │                 │
│         └───────────────────┼──────────────────┘                │
│                             │                                    │
│                             ▼                                    │
│  ┌──────────────────────────────────────────────────────────┐  │
│  │                  Context Assembler                        │  │
│  │                                                           │  │
│  │  1. System prompt (agent personality, role)               │  │
│  │  2. Project context (from long-term memory)               │  │
│  │  3. Task context (current issue, requirements)            │  │
│  │  4. Relevant history (from short-term memory)             │  │
│  │  5. User message                                          │  │
│  │                                                           │  │
│  │  Total: Fit within context window limits                  │  │
│  └──────────────────────────────────────────────────────────┘  │
│                                                                  │
└─────────────────────────────────────────────────────────────────┘
```

**Context Compression Strategy:**
```python
class ContextManager:
    """Manages agent context to fit within LLM limits."""

    MAX_CONTEXT_TOKENS = 100_000  # Leave room for response

    async def build_context(
        self,
        agent: AgentInstance,
        task: Task,
        user_message: str
    ) -> list[Message]:
        # Fixed costs
        system_prompt = self._get_system_prompt(agent)  # ~2K tokens
        task_context = self._get_task_context(task)     # ~1K tokens

        # Variable budget
        remaining = self.MAX_CONTEXT_TOKENS - token_count(system_prompt, task_context, user_message)

        # Allocate remaining to memories
        long_term = await self._query_long_term(agent, task, budget=remaining * 0.4)
        short_term = await self._get_short_term(agent, budget=remaining * 0.4)
        episodic = await self._get_relevant_episodes(agent, task, budget=remaining * 0.2)

        return self._assemble_messages(
            system_prompt, task_context, long_term, short_term, episodic, user_message
        )
```

**Conversation Summarization:**
- After every N turns (e.g., 10), summarize conversation and archive
- Use smaller/cheaper model for summarization
- Store summaries in pgvector for semantic retrieval

### Recommendation

Implement a **tiered memory system** with automatic context compression and semantic retrieval. Use Redis for hot short-term memory, pgvector for cold long-term memory, and automatic summarization to prevent context overflow.

---

## 2. Cross-Project Knowledge Sharing

### The Challenge

Each project has isolated knowledge, but agents could benefit from cross-project learnings:
- Common patterns (authentication, testing, CI/CD)
- Technology expertise (how to configure Kubernetes)
- Anti-patterns (what didn't work before)

### Analysis

**Privacy Considerations:**
- Client data must remain isolated (contractual, legal)
- Technical patterns are generally shareable
- Need clear data classification

**Knowledge Categories:**
| Category | Scope | Examples |
|----------|-------|----------|
| **Client Data** | Project-only | Requirements, business logic, code |
| **Technical Patterns** | Global | Best practices, configurations |
| **Agent Learnings** | Global | What approaches worked/failed |
| **Anti-patterns** | Global | Common mistakes to avoid |

### Proposed Architecture

```
┌─────────────────────────────────────────────────────────────────┐
│                    Knowledge Graph                               │
├─────────────────────────────────────────────────────────────────┤
│                                                                  │
│  ┌─────────────────────────────────────────────────────────┐   │
│  │                   GLOBAL KNOWLEDGE                       │   │
│  │  ┌─────────────┐  ┌─────────────┐  ┌─────────────┐      │   │
│  │  │  Patterns   │  │ Anti-patterns│  │  Expertise  │      │   │
│  │  │   Library   │  │   Library   │  │   Index     │      │   │
│  │  └─────────────┘  └─────────────┘  └─────────────┘      │   │
│  └─────────────────────────────────────────────────────────┘   │
│                             ▲                                    │
│                             │ Curated extraction                 │
│                             │                                    │
│  ┌─────────────┐  ┌─────────────┐  ┌─────────────┐             │
│  │  Project A  │  │  Project B  │  │  Project C  │             │
│  │  Knowledge  │  │  Knowledge  │  │  Knowledge  │             │
│  │  (Isolated) │  │  (Isolated) │  │  (Isolated) │             │
│  └─────────────┘  └─────────────┘  └─────────────┘             │
│                                                                  │
└─────────────────────────────────────────────────────────────────┘
```

**Knowledge Extraction Pipeline:**
```python
class KnowledgeExtractor:
    """Extracts shareable learnings from project work."""

    async def extract_learnings(self, project_id: str) -> list[Learning]:
        """
        Run periodically or after sprints to extract learnings.
        Human review required before promoting to global.
        """
        # Get completed work
        completed_issues = await self.get_completed_issues(project_id)

        # Extract patterns using LLM
        patterns = await self.llm.extract_patterns(
            completed_issues,
            categories=["architecture", "testing", "deployment", "security"]
        )

        # Classify privacy
        for pattern in patterns:
            pattern.privacy_level = await self.llm.classify_privacy(pattern)

        # Return only shareable patterns for review
        return [p for p in patterns if p.privacy_level == "public"]
```

### Recommendation

Implement **privacy-aware knowledge extraction** with human review gate. Project knowledge stays isolated by default; only explicitly approved patterns flow to global knowledge.

---

## 3. Agent Specialization vs Generalization Trade-offs

### The Challenge

Should each agent type be highly specialized (depth) or have overlapping capabilities (breadth)?

### Analysis

**Specialization Benefits:**
- Deeper expertise in domain
- Cleaner system prompts
- Less confusion about responsibilities
- Easier to optimize prompts per role

**Generalization Benefits:**
- Fewer agent types to maintain
- Smoother handoffs (shared context)
- More flexible team composition
- Graceful degradation if agent unavailable

**Current Agent Types (10):**
| Role | Primary Domain | Potential Overlap |
|------|---------------|-------------------|
| Product Owner | Requirements | Business Analyst |
| Business Analyst | Documentation | Product Owner |
| Project Manager | Planning | Product Owner |
| Software Architect | Design | Senior Engineer |
| Software Engineer | Coding | Architect, QA |
| UI/UX Designer | Interface | Frontend Engineer |
| QA Engineer | Testing | Software Engineer |
| DevOps Engineer | Infrastructure | Senior Engineer |
| AI/ML Engineer | ML/AI | Software Engineer |
| Security Expert | Security | All |

### Proposed Approach: Layered Specialization

```
┌─────────────────────────────────────────────────────────────────┐
│                   Agent Capability Layers                        │
├─────────────────────────────────────────────────────────────────┤
│                                                                  │
│  Layer 3: Role-Specific Expertise                                │
│  ┌─────────┐ ┌─────────┐ ┌─────────┐ ┌─────────┐               │
│  │ Product │ │ Architect│ │Engineer │ │   QA    │               │
│  │ Owner   │ │         │ │         │ │         │               │
│  └────┬────┘ └────┬────┘ └────┬────┘ └────┬────┘               │
│       │           │           │           │                      │
│  Layer 2: Shared Professional Skills                             │
│  ┌──────────────────────────────────────────────────────┐       │
│  │ Technical Communication | Code Understanding | Git   │       │
│  │ Documentation | Research | Problem Decomposition     │       │
│  └──────────────────────────────────────────────────────┘       │
│                             │                                    │
│  Layer 1: Foundation Model Capabilities                          │
│  ┌──────────────────────────────────────────────────────┐       │
│  │ Reasoning | Analysis | Writing | Coding (LLM Base)   │       │
│  └──────────────────────────────────────────────────────┘       │
│                                                                  │
└─────────────────────────────────────────────────────────────────┘
```

**Capability Inheritance:**
```python
class AgentTypeBuilder:
    """Builds agent types with layered capabilities."""

    BASE_CAPABILITIES = [
        "reasoning", "analysis", "writing", "coding_assist"
    ]

    PROFESSIONAL_SKILLS = [
        "technical_communication", "code_understanding",
        "git_operations", "documentation", "research"
    ]

    ROLE_SPECIFIC = {
        "ENGINEER": ["code_generation", "code_review", "testing", "debugging"],
        "ARCHITECT": ["system_design", "adr_writing", "tech_selection"],
        "QA": ["test_planning", "test_automation", "bug_reporting"],
        # ...
    }

    def build_capabilities(self, role: AgentRole) -> list[str]:
        return (
            self.BASE_CAPABILITIES +
            self.PROFESSIONAL_SKILLS +
            self.ROLE_SPECIFIC[role]
        )
```

### Recommendation

Adopt **layered specialization** where all agents share foundational and professional capabilities, with role-specific expertise on top. This enables smooth collaboration while maintaining clear responsibilities.

---

## 4. Human-Agent Collaboration Model

### The Challenge

Beyond approval gates, how do humans effectively collaborate with autonomous agents during active work?

### Interaction Patterns

| Pattern | Use Case | Frequency |
|---------|----------|-----------|
| **Approval** | Confirm before action | Per checkpoint |
| **Guidance** | Steer direction | On-demand |
| **Override** | Correct mistake | Rare |
| **Pair Working** | Work together | Optional |
| **Review** | Evaluate output | Post-completion |

### Proposed Collaboration Interface

```
┌─────────────────────────────────────────────────────────────────┐
│                Human-Agent Collaboration Dashboard               │
├─────────────────────────────────────────────────────────────────┤
│                                                                  │
│  ┌─────────────────────────────────────────────────────────┐   │
│  │                    Activity Stream                       │   │
│  │  ────────────────────────────────────────────────────── │   │
│  │  [10:23] Dave (Engineer) is implementing login API      │   │
│  │  [10:24] Dave created auth/service.py                   │   │
│  │  [10:25] Dave is writing unit tests                     │   │
│  │  [LIVE] Dave: "I'm adding JWT validation. Using HS256..." │  │
│  └─────────────────────────────────────────────────────────┘   │
│                                                                  │
│  ┌─────────────────────────────────────────────────────────┐   │
│  │                   Intervention Panel                     │   │
│  │                                                         │   │
│  │  [💬 Chat]  [⏸️ Pause]  [↩️ Undo Last]  [📝 Guide]     │   │
│  │                                                         │   │
│  │  Quick Guidance:                                        │   │
│  │  ┌─────────────────────────────────────────────────┐   │   │
│  │  │ "Use RS256 instead of HS256 for JWT signing"    │   │   │
│  │  │                                    [Send] 📤    │   │   │
│  │  └─────────────────────────────────────────────────┘   │   │
│  └─────────────────────────────────────────────────────────┘   │
│                                                                  │
└─────────────────────────────────────────────────────────────────┘
```

**Intervention API:**
```python
@router.post("/agents/{agent_id}/intervene")
async def intervene(
    agent_id: UUID,
    intervention: InterventionRequest,
    current_user: User = Depends(get_current_user)
):
    """Allow human to intervene in agent work."""
    match intervention.type:
        case "pause":
            await orchestrator.pause_agent(agent_id)
        case "resume":
            await orchestrator.resume_agent(agent_id)
        case "guide":
            await orchestrator.send_guidance(agent_id, intervention.message)
        case "undo":
            await orchestrator.undo_last_action(agent_id)
        case "override":
            await orchestrator.override_decision(agent_id, intervention.decision)
```

### Recommendation

Build a **real-time collaboration dashboard** with intervention capabilities. Humans should be able to observe, guide, pause, and correct agents without stopping the entire workflow.

---

## 5. Testing Strategy for Autonomous AI Systems

### The Challenge

Traditional testing (unit, integration, E2E) doesn't capture autonomous agent behavior. How do we ensure quality?

### Testing Pyramid for AI Agents

```
                    ▲
                   ╱ ╲
                  ╱   ╲
                 ╱ E2E ╲         Agent Scenarios
                ╱ Agent ╲        (Full workflows)
               ╱─────────╲
              ╱ Integration╲     Tool + LLM Integration
             ╱ (with mocks) ╲    (Deterministic responses)
            ╱─────────────────╲
           ╱  Unit Tests       ╲  Orchestrator, Services
          ╱  (no LLM needed)    ╲ (Pure logic)
         ╱───────────────────────╲
        ╱   Prompt Testing         ╲ System prompt evaluation
       ╱   (LLM evals)              ╲(Quality metrics)
      ╱─────────────────────────────╲
```

### Test Categories

**1. Prompt Testing (Eval Framework):**
```python
class PromptEvaluator:
    """Evaluate system prompt quality."""

    TEST_CASES = [
        EvalCase(
            name="requirement_extraction",
            input="Client wants a mobile app for food delivery",
            expected_behaviors=[
                "asks clarifying questions",
                "identifies stakeholders",
                "considers non-functional requirements"
            ]
        ),
        EvalCase(
            name="code_review_thoroughness",
            input="Review this PR: [vulnerable SQL code]",
            expected_behaviors=[
                "identifies SQL injection",
                "suggests parameterized queries",
                "mentions security best practices"
            ]
        )
    ]

    async def evaluate(self, agent_type: AgentType) -> EvalReport:
        results = []
        for case in self.TEST_CASES:
            response = await self.llm.complete(
                system=agent_type.system_prompt,
                user=case.input
            )
            score = await self.judge_response(response, case.expected_behaviors)
            results.append(score)
        return EvalReport(results)
```

**2. Integration Testing (Mock LLM):**
```python
@pytest.fixture
def mock_llm():
    """Deterministic LLM responses for integration tests."""
    responses = {
        "analyze requirements": "...",
        "generate code": "def hello(): return 'world'",
        "review code": "LGTM"
    }
    return MockLLM(responses)

async def test_story_implementation_workflow(mock_llm):
    """Test full workflow with predictable responses."""
    orchestrator = AgentOrchestrator(llm=mock_llm)

    result = await orchestrator.execute_workflow(
        workflow="implement_story",
        inputs={"story_id": "TEST-123"}
    )

    assert result.status == "completed"
    assert "hello" in result.artifacts["code"]
```

**3. Agent Scenario Testing:**
```python
class AgentScenarioTest:
    """End-to-end agent behavior testing."""

    @scenario("engineer_handles_bug_report")
    async def test_bug_resolution(self):
        """Engineer agent should fix bugs correctly."""
        # Setup
        project = await create_test_project()
        engineer = await spawn_agent("engineer", project)

        # Act
        bug = await create_issue(
            project,
            title="Login button not working",
            type="bug"
        )
        result = await engineer.handle(bug)

        # Assert
        assert result.pr_created
        assert result.tests_pass
        assert "button" in result.changes_summary.lower()
```

### Recommendation

Implement a **multi-layer testing strategy** with prompt evals, deterministic integration tests, and scenario-based agent testing. Use LLM-as-judge for evaluating open-ended responses.

---

## 6. Rollback and Recovery

### The Challenge

Autonomous agents will make mistakes. How do we recover gracefully?

### Error Categories

| Category | Example | Recovery Strategy |
|----------|---------|-------------------|
| **Reversible** | Wrong code generated | Revert commit, regenerate |
| **Partially Reversible** | Merged bad PR | Revert PR, fix, re-merge |
| **Non-reversible** | Deployed to production | Forward-fix or rollback deploy |
| **External Side Effects** | Email sent to client | Apology + correction |

### Recovery Architecture

```
┌─────────────────────────────────────────────────────────────────┐
│                    Recovery System                               │
├─────────────────────────────────────────────────────────────────┤
│                                                                  │
│  ┌─────────────────────────────────────────────────────────┐   │
│  │                    Action Log                            │   │
│  │  ┌──────────────────────────────────────────────────┐   │   │
│  │  │ Action ID | Agent | Type | Reversible | State    │   │   │
│  │  ├──────────────────────────────────────────────────┤   │   │
│  │  │ a-001 | Dave | commit | Yes | completed          │   │   │
│  │  │ a-002 | Dave | push | Yes | completed            │   │   │
│  │  │ a-003 | Dave | create_pr | Yes | completed       │   │   │
│  │  │ a-004 | Kate | merge_pr | Partial | completed    │   │   │
│  │  └──────────────────────────────────────────────────┘   │   │
│  └─────────────────────────────────────────────────────────┘   │
│                                                                  │
│  ┌─────────────────────────────────────────────────────────┐   │
│  │                 Rollback Engine                          │   │
│  │                                                         │   │
│  │  rollback_to(action_id) -> Reverses all actions after   │   │
│  │  undo_action(action_id) -> Reverses single action       │   │
│  │  compensate(action_id) -> Creates compensating action   │   │
│  │                                                         │   │
│  └─────────────────────────────────────────────────────────┘   │
│                                                                  │
└─────────────────────────────────────────────────────────────────┘
```

**Action Logging:**
```python
class ActionLog:
    """Immutable log of all agent actions for recovery."""

    async def record(
        self,
        agent_id: UUID,
        action_type: str,
        inputs: dict,
        outputs: dict,
        reversible: bool,
        reverse_action: str | None = None
    ) -> ActionRecord:
        record = ActionRecord(
            id=uuid4(),
            agent_id=agent_id,
            action_type=action_type,
            inputs=inputs,
            outputs=outputs,
            reversible=reversible,
            reverse_action=reverse_action,
            timestamp=datetime.utcnow()
        )
        await self.db.add(record)
        return record

    async def rollback_to(self, action_id: UUID) -> RollbackResult:
        """Rollback all actions after the given action."""
        actions = await self.get_actions_after(action_id)

        results = []
        for action in reversed(actions):
            if action.reversible:
                result = await self._execute_reverse(action)
                results.append(result)
            else:
                results.append(RollbackSkipped(action, reason="non-reversible"))

        return RollbackResult(results)
```

**Compensation Pattern:**
```python
class CompensationEngine:
    """Handles compensating actions for non-reversible operations."""

    COMPENSATIONS = {
        "email_sent": "send_correction_email",
        "deployment": "rollback_deployment",
        "external_api_call": "create_reversal_request"
    }

    async def compensate(self, action: ActionRecord) -> CompensationResult:
        if action.action_type in self.COMPENSATIONS:
            compensation = self.COMPENSATIONS[action.action_type]
            return await self._execute_compensation(compensation, action)
        else:
            return CompensationResult(
                status="manual_required",
                message=f"No automatic compensation for {action.action_type}"
            )
```

### Recommendation

Implement **comprehensive action logging** with rollback capabilities. Define compensation strategies for non-reversible actions. Enable point-in-time recovery for project state.

---

## 7. Security Considerations for Autonomous Agents

### Threat Model

| Threat | Risk | Mitigation |
|--------|------|------------|
| Agent executes malicious code | High | Sandboxed execution, code review gates |
| Agent exfiltrates data | High | Network isolation, output filtering |
| Prompt injection via user input | Medium | Input sanitization, prompt hardening |
| Agent credential abuse | Medium | Least-privilege tokens, short TTL |
| Agent collusion | Low | Independent agent instances, monitoring |

### Security Architecture

```
┌─────────────────────────────────────────────────────────────────┐
│                    Security Layers                               │
├─────────────────────────────────────────────────────────────────┤
│                                                                  │
│  Layer 4: Output Filtering                                       │
│  ┌─────────────────────────────────────────────────────────┐   │
│  │ - Code scan before commit                               │   │
│  │ - Secrets detection                                      │   │
│  │ - Policy compliance check                                │   │
│  └─────────────────────────────────────────────────────────┘   │
│                                                                  │
│  Layer 3: Action Authorization                                   │
│  ┌─────────────────────────────────────────────────────────┐   │
│  │ - Role-based permissions                                │   │
│  │ - Project scope enforcement                              │   │
│  │ - Sensitive action approval                              │   │
│  └─────────────────────────────────────────────────────────┘   │
│                                                                  │
│  Layer 2: Input Sanitization                                     │
│  ┌─────────────────────────────────────────────────────────┐   │
│  │ - Prompt injection detection                            │   │
│  │ - Content filtering                                      │   │
│  │ - Schema validation                                      │   │
│  └─────────────────────────────────────────────────────────┘   │
│                                                                  │
│  Layer 1: Infrastructure Isolation                               │
│  ┌─────────────────────────────────────────────────────────┐   │
│  │ - Container sandboxing                                   │   │
│  │ - Network segmentation                                   │   │
│  │ - File system restrictions                               │   │
│  └─────────────────────────────────────────────────────────┘   │
│                                                                  │
└─────────────────────────────────────────────────────────────────┘
```

### Recommendation

Implement **defense-in-depth** with multiple security layers. Assume agents can be compromised and design for containment.

---

## Summary of Recommendations

| Area | Recommendation | Priority |
|------|----------------|----------|
| Memory | Tiered memory with context compression | High |
| Knowledge | Privacy-aware extraction with human gate | Medium |
| Specialization | Layered capabilities with role-specific top | Medium |
| Collaboration | Real-time dashboard with intervention | High |
| Testing | Multi-layer with prompt evals | High |
| Recovery | Action logging with rollback engine | High |
| Security | Defense-in-depth, assume compromise | High |

---

## Next Steps

1. **Validate with spike research** - Update based on spike findings
2. **Create detailed ADRs** - For memory, recovery, security
3. **Prototype critical paths** - Memory system, rollback engine
4. **Security review** - External audit before production

---

*This document captures architectural thinking to guide implementation. It should be updated as spikes complete and design evolves.*