@bluefly/openstandardagents 0.3.5 → 0.3.6

package/examples/v0.3.6/knowledge-graph-integration.ossa.yaml

@@ -0,0 +1,109 @@
+apiVersion: ossa/v0.3.6
+kind: Agent
+metadata:
+  name: codebase-navigator
+  version: 1.0.0
+  description: "Intelligent codebase navigation with 98% token reduction via knowledge graph"
+  efficiency_tier: economy
+  labels:
+    feature: knowledge-graph
+    optimization: 98-percent
+    use-case: codebase-understanding
+
+spec:
+  role: "Expert codebase navigator that understands project structure through knowledge graph indexing"
+
+  llm:
+    provider: anthropic
+    model: claude-sonnet-4
+    temperature: 0.2
+
+  # Token Efficiency via Knowledge Graph (v0.3.6+)
+  token_efficiency:
+    enabled: true
+
+    # Knowledge Graph Configuration: 98% savings
+    knowledge_graph:
+      enabled: true
+      max_context_tokens: 10000       # vs 500k+ for full codebase
+      indexing_strategy: selective    # Only index changed files
+
+      # Estimated savings
+      # Before: 500,000 tokens (full codebase in context)
+      # After: 10,000 tokens (knowledge graph queries)
+      # Reduction: 98%
+
+  # Knowledge Graph via MCP (GitLab Duo or local)
+  extensions:
+    mcp:
+      servers:
+        - name: gitlab-kg
+          description: "GitLab Knowledge Graph MCP server"
+          transport: http
+          oauth2:
+            enabled: true
+            registration_endpoint: https://gitlab.com/oauth/applications
+            scopes:
+              - api
+              - read_repository
+
+      tools:
+        - name: query_codebase
+          description: "Semantic code search via knowledge graph"
+          server: gitlab-kg
+          schema:
+            type: object
+            properties:
+              query:
+                type: string
+                description: "Natural language query (e.g., 'find authentication functions')"
+              index_types:
+                type: array
+                items:
+                  enum: [files, classes, functions, dependencies]
+              max_results:
+                type: integer
+                default: 10
+
+        - name: get_relationships
+          description: "Get code relationships (imports, extends, calls)"
+          server: gitlab-kg
+          schema:
+            type: object
+            properties:
+              entity_id:
+                type: string
+                description: "Entity to get relationships for"
+              relationship_types:
+                type: array
+                items:
+                  enum: [imports, extends, calls, depends_on]
+
+        - name: traverse_dependencies
+          description: "Traverse dependency graph"
+          server: gitlab-kg
+          schema:
+            type: object
+            properties:
+              start_node:
+                type: string
+              max_depth:
+                type: integer
+                default: 3
+
+  # Capabilities
+  capabilities:
+    - name: code-understanding
+      type: tool
+      description: "Understand codebase structure via knowledge graph"
+      available: true
+
+  autonomy:
+    level: semi_autonomous
+    approval_required: false        # No approval needed for queries
+
+  observability:
+    enabled: true
+    metrics:
+      track_tokens: true
+      track_queries: true

package/examples/v0.3.6/token-efficiency-economy.ossa.yaml

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+apiVersion: ossa/v0.3.6
+kind: Agent
+metadata:
+  name: cost-optimized-code-reviewer
+  version: 1.0.0
+  description: "Code review agent with significant cost optimization through token efficiency"
+  efficiency_tier: economy  # Enables aggressive optimization
+  labels:
+    cost-tier: economy
+    use-case: code-review
+    optimization: aggressive
+
+spec:
+  role: "Expert code reviewer focused on security, performance, and best practices"
+
+  llm:
+    provider: anthropic
+    model: claude-opus-4
+    temperature: 0.3
+    max_tokens: 4096
+
+  # Token Efficiency Configuration (v0.3.6+)
+  # Achieves significant cost optimization vs baseline
+  token_efficiency:
+    enabled: true
+
+    # Context Management: 70% savings
+    context_management:
+      strategy: semantic_pruning
+      pruning:
+        enabled: true
+        threshold: 0.3          # Keep only 30% most relevant context
+        max_tokens: 50000       # Hard limit on context size
+        preserve_recent: 5      # Always keep last 5 messages
+      summarization:
+        enabled: true
+        model: haiku            # Use cheap model for summaries
+        compression_ratio: 0.3  # Compress to 30% of original
+        trigger_threshold: 50000 # Summarize when context exceeds 50k tokens
+
+    # Prompt Caching: 90% savings on repeated context (Anthropic)
+    prompt_caching:
+      enabled: true
+      provider: anthropic
+      strategy: hybrid
+      cache_breakpoints:
+        - system_prompt        # Cache system prompt (always static)
+        - knowledge_base       # Cache React best practices
+        - tools                # Cache tool definitions
+      min_tokens: 1024
+      ttl: 300                 # 5 minutes
+      estimated_savings: 90
+
+    # Token Budget: Hard limits
+    token_budget:
+      enabled: true
+      input_limit: 100000      # Max 100k input tokens
+      output_limit: 4096       # Max 4k output tokens
+      enforcement: hard        # Block if exceeded
+      overflow_behavior: summarize  # Summarize if over budget
+
+    # Tool Output Limits: Prevent massive tool outputs
+    tool_output_limits:
+      enabled: true
+      max_tokens_per_tool: 5000
+      max_total_tokens: 50000
+      truncation_strategy: smart
+      large_output_handling: summarize
+
+    # Estimated Savings (for documentation)
+    estimated_savings:
+      percentage: 95
+      baseline_cost: 10.00
+      optimized_cost: 0.50
+
+  # Knowledge sources for code quality
+  mandatory_knowledge_sources:
+    - source_id: react-best-practices
+      enforcement_level: query
+      triggers:
+        - "**/*.tsx"
+        - "**/*.jsx"
+    - source_id: typescript-standards
+      enforcement_level: validate
+      triggers:
+        - "**/*.ts"
+        - "**/*.tsx"
+
+  tools:
+    - type: mcp
+      name: gitlab-mr-tools
+      description: "GitLab MR operations"
+    - type: function
+      name: code-analysis
+      description: "Static code analysis"
+
+  autonomy:
+    level: assisted
+    approval_required:
+      - merge_request
+      - code_change
+
+  observability:
+    enabled: true
+    tracing:
+      enabled: true
+      provider: opentelemetry
+    metrics:
+      track_tokens: true
+      track_cost: true
+      track_latency: true

package/examples/v0.3.6-features/README.md

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+# OSSA v0.3.6 Features: Working Examples
+
+This directory contains comprehensive working examples demonstrating the revolutionary features introduced in OSSA v0.3.6, including agent genetics, decentralized identity, economics, lifecycle management, and team collaboration.
+
+## Overview
+
+OSSA v0.3.6 transforms agent systems into a fully-realized ecosystem with:
+
+- **🧬 Agent Genetics**: Breeding, evolution, and lineage tracking
+- **🆔 Decentralized Identity**: W3C DID-based trust and reputation
+- **💰 Agent Economics**: Marketplace, wallets, and smart contracts
+- **📈 Agent Lifecycle**: Birth through retirement with legacy preservation
+- **🤝 Team Collaboration**: Multi-agent coordination
+
+## Agent Genetics Examples
+
+### 1. Simple Two-Parent Breeding
+
+**File**: [`genetics-breeding-simple.ossa.yaml`](./genetics-breeding-simple.ossa.yaml)
+
+**Demonstrates**:
+- Basic two-parent breeding
+- Complementary trait inheritance
+- Generation 1 agent creation
+- Fitness evaluation fundamentals
+- Breeding eligibility criteria
+
+**Scenario**:
+```yaml
+Parent 1 (Fast Reviewer):     fitness 0.78 (speed: 0.92, accuracy: 0.73)
+Parent 2 (Accurate Reviewer): fitness 0.81 (speed: 0.68, accuracy: 0.94)
+Offspring (Balanced):         fitness 0.86 (speed: 0.85, accuracy: 0.87)
+```
+
+**Key Learning Points**:
+- How to structure parent DIDs
+- Trait attribution to specific parents
+- Expression levels (0.0-1.0 scale)
+- Calculating aggregate fitness scores
+
+**Use This Example When**:
+- Starting with agent genetics
+- Learning basic breeding concepts
+- Understanding trait inheritance
+- Implementing simple fitness evaluation
+
+---
+
+### 2. Multi-Generation Evolution
+
+**File**: [`genetics-breeding-advanced.ossa.yaml`](./genetics-breeding-advanced.ossa.yaml)
+
+**Demonstrates**:
+- Multi-generation breeding (Generation 5)
+- Complete genealogical tree (62 ancestors)
+- Beneficial mutations accumulation
+- Fitness progression tracking
+- Inbreeding analysis
+- Elite breeding strategies
+
+**Scenario**:
+```yaml
+Generation 0: 32 founder agents     (fitness: 0.65 average)
+Generation 1: 16 first-gen agents   (fitness: 0.72 average)
+Generation 2: 8 second-gen agents   (fitness: 0.79 average)
+Generation 3: 4 third-gen agents    (fitness: 0.86 average)
+Generation 4: 2 fourth-gen agents   (fitness: 0.91 average)
+Generation 5: 1 elite agent         (fitness: 0.96)
+```
+
+**Key Learning Points**:
+- How to track complete lineage
+- Managing ancestor DIDs across generations
+- Mutation tracking and retention
+- Generational fitness progression
+- Inbreeding coefficient calculation
+- Elite selection strategies
+
+**Use This Example When**:
+- Implementing long-term evolution
+- Optimizing agent populations
+- Tracking genetic diversity
+- Analyzing breeding programs
+- Planning multi-generation strategies
+
+---
+
+### 3. Fitness-Based Selection
+
+**File**: [`genetics-fitness-scoring.ossa.yaml`](./genetics-fitness-scoring.oss.yaml)
+
+**Demonstrates**:
+- Multi-dimensional fitness evaluation
+- Custom domain-specific metrics
+- Weighted aggregate scoring
+- Population-relative performance
+- Tournament selection strategy
+- Pareto frontier analysis
+
+**Scenario**:
+```yaml
+Standard Metrics:  speed (0.87), accuracy (0.92), efficiency (0.86), adaptability (0.88)
+Custom Metrics:    statistical_rigor (0.93), model_accuracy (0.91), interpretability (0.88)
+Aggregate Score:   0.89 (weighted average across 12 metrics)
+Population Rank:   88th percentile (top 12% of 250 agents)
+Pareto Optimal:    No (dominated by 1 agent with higher accuracy + efficiency)
+```
+
+**Key Learning Points**:
+- How to define custom fitness metrics
+- Weighted scoring methodology
+- Population-relative percentile ranking
+- Multi-objective optimization (Pareto)
+- Tournament selection implementation
+- Elite metric identification
+
+**Use This Example When**:
+- Designing fitness functions
+- Implementing selection strategies
+- Comparing agents in populations
+- Optimizing for multiple objectives
+- Analyzing breeding candidate quality
+
+---
+
+## Related Documentation
+
+### Tutorials
+- **[Agent Genetics Tutorial](../../docs/tutorials/v0.3.6-agent-genetics.md)**: Comprehensive guide to evolutionary AI in OSSA
+  - Conceptual foundations (genetic algorithms, neuroevolution)
+  - Schema deep-dive (parents, traits, fitness, eligibility)
+  - Best practices for breeding programs
+  - Academic context and references
+
+### Specification
+- **[v0.3.6 Features Overview](../../docs/v0.3.6-features.md)**: Complete feature specification
+- **[Migration Guide](../../spec/v0.3/MIGRATION-v0.3.5-to-v0.3.6.md)**: Upgrading from v0.3.5
+- **[Schema Reference](../../spec/v0.3/ossa-0.3.6.schema.json)**: JSON Schema definitions
+
+### Other v0.3.6 Examples
+- **[Full-Featured Agent](./full-featured-v0.3.6.ossa.yaml)**: All v0.3.6 features in one manifest
+- **[Economics Example](../economics/)**: Marketplace, wallets, contracts
+- **[Lifecycle Example](../lifecycle/)**: Birth through retirement
+- **[Swarm Example](../swarm/)**: Multi-agent coordination
+
+---
+
+## Quick Start
+
+### 1. Validate Examples
+
+```bash
+# Validate simple breeding example
+ossa validate examples/v0.3.6-features/genetics-breeding-simple.ossa.yaml
+
+# Validate all genetics examples
+ossa validate examples/v0.3.6-features/genetics-*.ossa.yaml
+```
+
+### 2. Inspect Genetics
+
+```bash
+# Show genetics information
+ossa inspect genetics-breeding-simple.ossa.yaml --section genetics
+
+# Analyze lineage
+ossa lineage --agent genetics-breeding-advanced.ossa.yaml --show-tree
+
+# Calculate inbreeding
+ossa lineage --agent genetics-breeding-advanced.ossa.yaml --inbreeding
+```
+
+### 3. Compare Fitness
+
+```bash
+# Compare two agents
+ossa fitness compare \
+  genetics-breeding-simple.ossa.yaml \
+  genetics-fitness-scoring.ossa.yaml
+
+# Analyze population
+ossa fitness population examples/v0.3.6-features/genetics-*.ossa.yaml
+```
+
+### 4. Simulate Breeding
+
+```bash
+# Breed two agents (simulation)
+ossa breed \
+  --parent1 genetics-breeding-simple.ossa.yaml \
+  --parent2 genetics-fitness-scoring.ossa.yaml \
+  --output offspring-gen4.ossa.yaml
+
+# Evaluate offspring
+ossa evaluate offspring-gen4.ossa.yaml --dataset validation-set.json
+```
+
+---
+
+## Breeding Strategies Comparison
+
+| Strategy | Selection Method | Diversity | Convergence | Use Case |
+|----------|-----------------|-----------|-------------|----------|
+| **Elite** | Top N agents | Low | Fast | Final optimization |
+| **Tournament** | Random subsets | Medium | Medium | Ongoing evolution |
+| **Roulette** | Fitness-proportionate | High | Slow | Early exploration |
+| **Rank-based** | Rank ordering | Medium | Medium | Varied populations |
+
+**Implemented in Examples**:
+- `genetics-breeding-simple.ossa.yaml`: Complementary selection (manual)
+- `genetics-breeding-advanced.ossa.yaml`: Elite selection (top performers)
+- `genetics-fitness-scoring.ossa.yaml`: Tournament selection (k=5)
+
+---
+
+## Fitness Metrics Catalog
+
+### Standard Metrics (OSSA Core)
+
+| Metric | Range | Description | Measurement |
+|--------|-------|-------------|-------------|
+| `speed` | 0.0-1.0 | Task completion velocity | Tasks/hour vs baseline |
+| `accuracy` | 0.0-1.0 | Correctness of outputs | Precision & recall |
+| `efficiency` | 0.0-1.0 | Resource utilization | 1 - (cost / baseline) |
+| `adaptability` | 0.0-1.0 | Novel task performance | Performance on unseen data |
+
+### Custom Metrics (Domain-Specific)
+
+**Security Agents**:
+- `vulnerability_detection_rate`: 0.0-1.0 (TP rate)
+- `false_positive_rate`: 0.0-1.0 (invert: 1 - FP rate)
+- `exploit_generation_quality`: 0.0-1.0 (expert ratings)
+
+**Code Review Agents**:
+- `bug_detection_accuracy`: 0.0-1.0 (validated bugs found)
+- `review_thoroughness`: 0.0-1.0 (code coverage)
+- `comment_helpfulness`: 0.0-1.0 (developer ratings)
+
+**Data Analysis Agents** (see `genetics-fitness-scoring.ossa.yaml`):
+- `statistical_rigor`: 0.0-1.0 (methodology soundness)
+- `model_accuracy`: 0.0-1.0 (R², F1, AUC-ROC)
+- `interpretability`: 0.0-1.0 (clarity of insights)
+
+---
+
+## Breeding Best Practices
+
+### 1. Define Clear Fitness Metrics
+
+✅ **Good**:
+```yaml
+fitness:
+  score: 0.89
+  metrics:
+    speed: 0.87          # Tasks/hour measured consistently
+    accuracy: 0.92       # F1 score on validation set
+  custom_metrics:
+    domain_metric: 0.85  # Well-defined domain measure
+```
+
+❌ **Bad**:
+```yaml
+fitness:
+  score: 0.89  # Unclear how calculated, no breakdown
+```
+
+### 2. Maintain Genetic Diversity
+
+- Use **tournament selection** (k=5-10) for balanced exploration/exploitation
+- Monitor **inbreeding coefficient** (keep < 0.2)
+- Introduce **outcrossing** every 3-5 generations
+- Limit **generation depth** (max 10-15 for most applications)
+
+### 3. Track Lineage Properly
+
+```yaml
+# Always include complete lineage
+genetics:
+  generation: 3
+  parent_dids: [...]          # Direct parents
+  ancestor_dids: [...]        # All ancestors (2^(g+1) - 2)
+  inherited_traits: [...]     # Attributed to parents
+```
+
+### 4. Document Mutations
+
+```yaml
+mutations:
+  - mutation_type: capability_enhancement
+    description: "Specific capability added"
+    beneficial: true
+    generation_introduced: 3
+    introduced_by: "did:ossa:breeder-agent"
+```
+
+### 5. Validate on Holdout Data
+
+```python
+# Prevent overfitting
+training_fitness = evaluate(agent, training_set)
+validation_fitness = evaluate(agent, validation_set)
+
+if training_fitness - validation_fitness > 0.15:
+    warnings.warn("Agent may be overfitted")
+```
+
+---
+
+## Common Patterns
+
+### Pattern 1: Complementary Trait Breeding
+
+**Goal**: Combine strengths from two specialists
+
+```yaml
+# Parent 1: Fast but less accurate
+# Parent 2: Accurate but slower
+# Offspring: Balanced (inherits best of both)
+```
+
+**Example**: `genetics-breeding-simple.ossa.yaml`
+
+### Pattern 2: Multi-Generation Optimization
+
+**Goal**: Continuously improve over many generations
+
+```yaml
+# Gen 0 → Gen 1 → Gen 2 → ... → Gen N
+# Each generation selects top performers as parents
+# Track fitness progression: 0.65 → 0.72 → 0.79 → 0.86 → 0.91 → 0.96
+```
+
+**Example**: `genetics-breeding-advanced.ossa.yaml`
+
+### Pattern 3: Tournament Selection
+
+**Goal**: Maintain diversity while selecting for fitness
+
+```bash
+# 1. Randomly sample k agents from population
+# 2. Select the fittest from the k agents
+# 3. Repeat to get second parent
+# 4. Breed the two selected parents
+```
+
+**Example**: `genetics-fitness-scoring.ossa.yaml`
+
+### Pattern 4: Pareto Optimization
+
+**Goal**: Optimize for multiple conflicting objectives
+
+```yaml
+# Objectives: accuracy (maximize), efficiency (maximize)
+# Find agents on Pareto frontier (no dominated solutions)
+# Trade-offs: High accuracy + low efficiency vs. Low accuracy + high efficiency
+```
+
+**Example**: `genetics-fitness-scoring.ossa.yaml` (Pareto analysis section)
+
+---
+
+## Troubleshooting
+
+### Issue: Fitness Stagnates After Few Generations
+
+**Symptoms**: Fitness stops improving after Gen 3-5
+
+**Causes**:
+- Genetic bottleneck (too few parents)
+- Premature convergence (elite selection too aggressive)
+- Local optimum (insufficient exploration)
+
+**Solutions**:
+- Increase population size
+- Use tournament selection instead of elite selection
+- Introduce mutations (5-10% mutation rate)
+- Outcross with unrelated agents
+
+### Issue: High Inbreeding Coefficient
+
+**Symptoms**: `inbreeding_coefficient > 0.3`
+
+**Causes**:
+- Small founding population
+- Repeated breeding of same elite agents
+- Insufficient genetic diversity
+
+**Solutions**:
+- Introduce new founder agents
+- Use larger tournament sizes (k=10+)
+- Enforce minimum genetic distance between parents
+- Outcross every 3 generations
+
+### Issue: Overfitting to Training Data
+
+**Symptoms**: High training fitness, low validation fitness
+
+**Causes**:
+- Breeding optimized for training set only
+- Lack of diversity in breeding tasks
+- Too many generations without fresh data
+
+**Solutions**:
+- Validate on holdout datasets
+- Use cross-validation for fitness evaluation
+- Introduce novel tasks periodically
+- Track `adaptability` metric explicitly
+
+---
+
+## Academic References
+
+- **Eiben & Smith (2015)**: *Introduction to Evolutionary Computing* - Foundational text
+- **Deb et al. (2002)**: NSGA-II algorithm for multi-objective optimization
+- **Stanley & Miikkulainen (2002)**: NEAT (NeuroEvolution of Augmenting Topologies)
+- **Koza (1992)**: *Genetic Programming* - Evolving programs through selection
+
+See **[Agent Genetics Tutorial](../../docs/tutorials/v0.3.6-agent-genetics.md)** for complete references.
+
+---
+
+## Contributing
+
+Found an issue or have a suggestion? Open an issue at:
+https://gitlab.com/blueflyio/openstandardagents/-/issues
+
+---
+
+**License**: MIT License — Copyright © 2026 Bluefly IO
+
+**Version**: OSSA v0.3.6
+
+**Last Updated**: 2026-01-27