fix: Update internal links for Diátaxis reorganization

GeneAI · claude · GeneAI · commit 2b7f710a8f3b · 2025-12-24T16:04:50.000-05:00
Fix broken documentation links after restructuring: - api-reference/ → reference/ - getting-started/ → tutorials/ - examples/ → tutorials/examples/ - Fix double path issues (tutorials/tutorials/) 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
diff --git a/docs/explanation/adaptive-learning.md b/docs/explanation/adaptive-learning.md
@@ -413,13 +413,13 @@ print(f"Learning velocity: {metrics['learning_velocity']}")  # How fast improvin
 
 ## Examples
 
-See the complete [Adaptive Learning System Example](../examples/adaptive-learning-system.md) for a full implementation.
+See the complete [Adaptive Learning System Example](../tutorials/examples/adaptive-learning-system.md) for a full implementation.
 
 ---
 
 ## See Also
 
 - [Multi-Agent Coordination](multi-agent-coordination.md) - Team patterns
-- [Adaptive Learning Example](../examples/adaptive-learning-system.md) - Full implementation
-- [Pattern Library API](../api-reference/pattern-library.md) - Pattern management
-- [EmpathyOS API](../api-reference/empathy-os.md) - Core configuration
+- [Adaptive Learning Example](../tutorials/examples/adaptive-learning-system.md) - Full implementation
+- [Pattern Library API](../reference/pattern-library.md) - Pattern management
+- [EmpathyOS API](../reference/empathy-os.md) - Core configuration
diff --git a/docs/explanation/multi-agent-philosophy.md b/docs/explanation/multi-agent-philosophy.md
@@ -492,8 +492,8 @@ session.signal("review_complete", {
 ## Next Steps
 
 - **[Short-Term Memory Reference](../SHORT_TERM_MEMORY.md)**: Complete API documentation
-- **[API Reference: Multi-Agent](../api-reference/multi-agent.md)**: Detailed class documentation
-- **[Example: Team Coordination](../examples/multi-agent-team-coordination.md)**: Full working example
+- **[API Reference: Multi-Agent](../reference/multi-agent.md)**: Detailed class documentation
+- **[Example: Team Coordination](../tutorials/examples/multi-agent-team-coordination.md)**: Full working example
 
 ---
 
diff --git a/docs/how-to/hipaa-compliance.md b/docs/how-to/hipaa-compliance.md
@@ -466,9 +466,9 @@ For a **100-bed hospital**:
 ## See Also
 
 - [Security Architecture](security-architecture.md) - Technical implementation details
-- [Healthcare Wizards](../api-reference/wizards.md) - PHI-aware AI assistants
-- [SBAR Example](../examples/sbar-clinical-handoff.md) - HIPAA-compliant handoff protocol
-- [LLM Toolkit](../api-reference/llm-toolkit.md) - Security API reference
+- [Healthcare Wizards](../reference/wizards.md) - PHI-aware AI assistants
+- [SBAR Example](../tutorials/examples/sbar-clinical-handoff.md) - HIPAA-compliant handoff protocol
+- [LLM Toolkit](../reference/llm-toolkit.md) - Security API reference
 
 ---
 
diff --git a/docs/how-to/multi-agent-coordination.md b/docs/how-to/multi-agent-coordination.md
@@ -503,7 +503,7 @@ print(f"Collaboration efficiency: {team_stats['collaboration_efficiency']:.0%}")
 
 ## Examples
 
-See the complete [Multi-Agent Team Coordination Example](../examples/multi-agent-team-coordination.md) for a full implementation with:
+See the complete [Multi-Agent Team Coordination Example](../tutorials/examples/multi-agent-team-coordination.md) for a full implementation with:
 
 - PR review automation
 - Automated test generation
@@ -516,6 +516,6 @@ See the complete [Multi-Agent Team Coordination Example](../examples/multi-agent
 ## See Also
 
 - [Adaptive Learning](adaptive-learning.md) - How agents learn
-- [Pattern Library API](../api-reference/pattern-library.md) - Pattern management
-- [Multi-Agent Example](../examples/multi-agent-team-coordination.md) - Full implementation
-- [EmpathyOS API](../api-reference/empathy-os.md) - Agent configuration
+- [Pattern Library API](../reference/pattern-library.md) - Pattern management
+- [Multi-Agent Example](../tutorials/examples/multi-agent-team-coordination.md) - Full implementation
+- [EmpathyOS API](../reference/empathy-os.md) - Agent configuration
diff --git a/docs/how-to/practical-patterns.md b/docs/how-to/practical-patterns.md
@@ -679,8 +679,8 @@ print(f"After 12 successes: {status['current_tier']}")
 
 ## Next Steps
 
-- **[API Reference](../api-reference/multi-agent.md)**: Full class documentation
-- **[Examples](../examples/multi-agent-team-coordination.md)**: Complete working examples
+- **[API Reference](../reference/multi-agent.md)**: Full class documentation
+- **[Examples](../tutorials/examples/multi-agent-team-coordination.md)**: Complete working examples
 - **[Philosophy](./multi-agent-philosophy.md)**: Understand the design principles
 
 ---
diff --git a/docs/how-to/security-architecture.md b/docs/how-to/security-architecture.md
@@ -370,6 +370,6 @@ def test_secrets_detection():
 ## See Also
 
 - [HIPAA Compliance Guide](hipaa-compliance.md) - Healthcare-specific requirements
-- [LLM Toolkit API](../api-reference/llm-toolkit.md) - Security API reference
-- [Industry Wizards](../api-reference/wizards.md) - Domain-specific security
-- [SBAR Example](../examples/sbar-clinical-handoff.md) - Healthcare security in action
+- [LLM Toolkit API](../reference/llm-toolkit.md) - Security API reference
+- [Industry Wizards](../reference/wizards.md) - Domain-specific security
+- [SBAR Example](../tutorials/examples/sbar-clinical-handoff.md) - Healthcare security in action
diff --git a/docs/how-to/short-term-memory-implementation.md b/docs/how-to/short-term-memory-implementation.md
@@ -543,8 +543,8 @@ new_agent.restore_collaboration_state(session_id=agent.session_id)
 ## Next Steps
 
 - **[Practical Patterns](./practical-patterns.md)**: Ready-to-use patterns for common scenarios
-- **[API Reference](../api-reference/multi-agent.md)**: Complete class documentation
-- **[Examples](../examples/multi-agent-team-coordination.md)**: Full working examples
+- **[API Reference](../reference/multi-agent.md)**: Complete class documentation
+- **[Examples](../tutorials/examples/multi-agent-team-coordination.md)**: Full working examples
 
 ---
 
diff --git a/docs/how-to/unified-memory-system.md b/docs/how-to/unified-memory-system.md
@@ -444,7 +444,7 @@ from empathy_os.memory.security import AuditLogger
 
 - **[Short-Term Memory Implementation](./short-term-memory-implementation.md)**: Detailed Redis setup
 - **[Security Architecture](./security-architecture.md)**: PII scrubbing, encryption, audit logging
-- **[API Reference: Memory](../api-reference/multi-agent.md)**: Complete class documentation
+- **[API Reference: Memory](../reference/multi-agent.md)**: Complete class documentation
 
 ---
 
diff --git a/docs/how-to/webhook-integration.md b/docs/how-to/webhook-integration.md
@@ -556,7 +556,7 @@ print(f"Failed deliveries: {stats['failed_count']}")
 
 ## Examples
 
-See the complete [Webhook Event Integration Example](../examples/webhook-event-integration.md) for implementations with:
+See the complete [Webhook Event Integration Example](../tutorials/examples/webhook-event-integration.md) for implementations with:
 
 - Slack notifications
 - JIRA ticket creation
@@ -568,6 +568,6 @@ See the complete [Webhook Event Integration Example](../examples/webhook-event-i
 
 ## See Also
 
-- [Webhook Example](../examples/webhook-event-integration.md) - Full implementation
+- [Webhook Example](../tutorials/examples/webhook-event-integration.md) - Full implementation
 - [Security Architecture](security-architecture.md) - Webhook security
-- [EmpathyOS API](../api-reference/empathy-os.md) - Webhook configuration
+- [EmpathyOS API](../reference/empathy-os.md) - Webhook configuration
diff --git a/docs/index.md b/docs/index.md
@@ -102,7 +102,7 @@ Webhooks for Slack, GitHub, JIRA, Datadog, and custom services.
 
     **Patient Handoffs**: Automated SBAR reports (60% time savings)
 
-    **Live demo coming soon** - See the [SBAR Example](examples/sbar-clinical-handoff.md) for complete code
+    **Live demo coming soon** - See the [SBAR Example](tutorials/examples/sbar-clinical-handoff.md) for complete code
 
     ```python
     from empathy_os import EmpathyOS
@@ -148,10 +148,14 @@ Webhooks for Slack, GitHub, JIRA, Datadog, and custom services.
 
 ## Documentation
 
-- **[Getting Started](getting-started/installation.md)**: Install and configure
-- **[Examples](examples/simple-chatbot.md)**: 5 comprehensive tutorials
-- **[API Reference](api-reference/index.md)**: Complete API documentation
-- **[Contributing](contributing.md)**: How to contribute
+Organized using the [Diátaxis framework](https://diataxis.fr/) for better discoverability:
+
+| Section | Purpose | Start Here |
+|---------|---------|------------|
+| **[Tutorials](tutorials/index.md)** | Learn by doing | [Quick Start](tutorials/quickstart.md) |
+| **[How-to](how-to/index.md)** | Solve specific tasks | [Agent Factory](how-to/agent-factory.md) |
+| **[Explanation](explanation/index.md)** | Understand concepts | [Philosophy](explanation/EMPATHY_PHILOSOPHY.md) |
+| **[Reference](reference/index.md)** | Look up details | [API Reference](reference/API_REFERENCE.md) |
 
 ---
 
@@ -190,31 +194,31 @@ Webhooks for Slack, GitHub, JIRA, Datadog, and custom services.
 
     Get up and running in 5 minutes
 
-    [:octicons-arrow-right-24: Quick Start](getting-started/quickstart.md)
+    [:octicons-arrow-right-24: Quick Start](tutorials/quickstart.md)
 
 -   :fontawesome-solid-robot:{ .lg .middle } **Examples**
 
     ---
 
     5 comprehensive tutorials with working code
 
-    [:octicons-arrow-right-24: See Examples](examples/simple-chatbot.md)
+    [:octicons-arrow-right-24: See Examples](tutorials/examples/simple-chatbot.md)
 
 -   :fontawesome-solid-hospital:{ .lg .middle } **Healthcare**
 
     ---
 
     HIPAA-compliant, $2M+ ROI
 
-    [:octicons-arrow-right-24: SBAR Example](examples/sbar-clinical-handoff.md)
+    [:octicons-arrow-right-24: SBAR Example](tutorials/examples/sbar-clinical-handoff.md)
 
 -   :material-book-open-variant:{ .lg .middle } **API Reference**
 
     ---
 
     Complete API documentation
 
-    [:octicons-arrow-right-24: API Docs](api-reference/index.md)
+    [:octicons-arrow-right-24: API Docs](reference/index.md)
 
 </div>
 
diff --git a/docs/reference/SHORT_TERM_MEMORY.md b/docs/reference/SHORT_TERM_MEMORY.md
@@ -367,9 +367,9 @@ print(f"Received {len(signals)} reviews")
 ## API Reference
 
 See the full API documentation:
-- [EmpathyOS](./api-reference/empathy-os.md)
-- [Multi-Agent Coordination](./api-reference/multi-agent.md)
-- [Persistence](./api-reference/persistence.md)
+- [EmpathyOS](empathy-os.md)
+- [Multi-Agent Coordination](multi-agent.md)
+- [Persistence](persistence.md)
 
 ---
 
diff --git a/docs/reference/config.md b/docs/reference/config.md
@@ -370,5 +370,5 @@ export EMPATHY_PATTERN_CONFIDENCE_THRESHOLD=0.70
 ## See Also
 
 - [EmpathyOS API](empathy-os.md)
-- [Quick Start Guide](../getting-started/quickstart.md)
-- [Configuration Examples](../getting-started/configuration.md)
+- [Quick Start Guide](../tutorials/quickstart.md)
+- [Configuration Examples](../reference/configuration.md)
diff --git a/docs/reference/configuration.md b/docs/reference/configuration.md
@@ -73,5 +73,5 @@ export EMPATHY_CONFIDENCE_THRESHOLD=0.75
 
 ## Next Steps
 
-- **[Examples](../examples/simple-chatbot.md)**: See configuration in action
-- **[API Reference](../api-reference/empathy-os.md)**: Complete API documentation
+- **[Examples](../tutorials/tutorials/examples/simple-chatbot.md)**: See configuration in action
+- **[API Reference](../reference/empathy-os.md)**: Complete API documentation
diff --git a/docs/reference/core.md b/docs/reference/core.md
@@ -343,4 +343,4 @@ elif response.level >= 4:
 - [EmpathyOS API](empathy-os.md)
 - [Configuration API](config.md)
 - [Pattern Library](pattern-library.md)
-- [Simple Chatbot Example](../examples/simple-chatbot.md)
+- [Simple Chatbot Example](../tutorials/tutorials/examples/simple-chatbot.md)
diff --git a/docs/reference/empathy-os.md b/docs/reference/empathy-os.md
@@ -214,4 +214,4 @@ See [Configuration API](config.md) for detailed configuration options.
 - [Configuration Reference](config.md)
 - [Core Data Structures](core.md)
 - [Pattern Library](pattern-library.md)
-- [Simple Chatbot Example](../examples/simple-chatbot.md)
+- [Simple Chatbot Example](../tutorials/tutorials/examples/simple-chatbot.md)
diff --git a/docs/reference/llm-toolkit.md b/docs/reference/llm-toolkit.md
@@ -545,5 +545,5 @@ llm = EmpathyLLM(
 
 - [EmpathyOS API](empathy-os.md)
 - [Configuration API](config.md)
-- [Healthcare SBAR Example](../examples/sbar-clinical-handoff.md)
+- [Healthcare SBAR Example](../tutorials/tutorials/examples/sbar-clinical-handoff.md)
 - [Security Architecture](../guides/security-architecture.md)
diff --git a/docs/reference/multi-agent.md b/docs/reference/multi-agent.md
@@ -430,5 +430,5 @@ if stats["most_used_strategy"] == "highest_confidence":
 
 - [Pattern Library](pattern-library.md) - Pattern storage and retrieval
 - [EmpathyOS](empathy-os.md) - Core agent API
-- [Multi-Agent Coordination Example](../examples/multi-agent-team-coordination.md)
+- [Multi-Agent Coordination Example](../tutorials/examples/multi-agent-team-coordination.md)
 - See the Memory System chapter for distributed memory concepts
diff --git a/docs/reference/pattern-library.md b/docs/reference/pattern-library.md
@@ -425,5 +425,5 @@ if best:
 
 - [EmpathyOS API](empathy-os.md)
 - [Persistence API](persistence.md)
-- [Multi-Agent Coordination Example](../examples/multi-agent-team-coordination.md)
-- [Adaptive Learning Example](../examples/adaptive-learning-system.md)
+- [Multi-Agent Coordination Example](../tutorials/examples/multi-agent-team-coordination.md)
+- [Adaptive Learning Example](../tutorials/examples/adaptive-learning-system.md)
diff --git a/docs/reference/persistence.md b/docs/reference/persistence.md
@@ -464,4 +464,4 @@ def batch_save_patterns(patterns, db_path):
 - [Pattern Library API](pattern-library.md)
 - [EmpathyOS API](empathy-os.md)
 - [Configuration API](config.md)
-- [CLI Export/Import Commands](../getting-started/quickstart.md#cli-commands)
+- [CLI Export/Import Commands](../tutorials/quickstart.md#cli-commands)
diff --git a/docs/reference/wizards.md b/docs/reference/wizards.md
@@ -107,7 +107,7 @@ Domain-specific AI assistants with built-in security, compliance, and industry b
         4. ✅ Implement access controls
         5. ✅ Sign Business Associate Agreement with LLM provider
 
-    **See Also:** [SBAR Clinical Handoff Example](../examples/sbar-clinical-handoff.md)
+    **See Also:** [SBAR Clinical Handoff Example](../tutorials/tutorials/examples/sbar-clinical-handoff.md)
 
 === ":fontawesome-solid-building-columns: Finance"
 
@@ -522,5 +522,5 @@ result = await wizard.process(
 
 - [LLM Toolkit](llm-toolkit.md) - Core LLM functionality
 - [Security Architecture](../guides/security-architecture.md) - Security implementation details
-- [SBAR Example](../examples/sbar-clinical-handoff.md) - Healthcare wizard in action
+- [SBAR Example](../tutorials/tutorials/examples/sbar-clinical-handoff.md) - Healthcare wizard in action
 - [Configuration](config.md) - Wizard configuration options
diff --git a/docs/tutorials/examples/simple-chatbot.md b/docs/tutorials/examples/simple-chatbot.md
@@ -639,4 +639,4 @@ memory = UnifiedMemory(redis_url=None)
 
 ---
 
-**Need help?** See the [API Reference](../api-reference/index.md) or [Short-Term Memory Reference](../SHORT_TERM_MEMORY.md).
+**Need help?** See the [API Reference](../reference/index.md) or [Short-Term Memory Reference](../SHORT_TERM_MEMORY.md).
diff --git a/docs/tutorials/quickstart.md b/docs/tutorials/quickstart.md
@@ -179,7 +179,7 @@ for step in result.first_steps:
 - **[Guides](../guides/multi-agent-philosophy.md)** - Learn the philosophy behind multi-agent coordination
 - **[Implementation](../guides/short-term-memory-implementation.md)** - Build your own coordinating agents
 - **[Practical Patterns](../guides/practical-patterns.md)** - Ready-to-use patterns with measured benefits
-- **[Examples](../examples/multi-agent-team-coordination.md)** - Full working code samples
+- **[Examples](examples/multi-agent-team-coordination.md)** - Full working code samples
 
 ---
 
