docs: fix GitHub URLs and navigation links in foundational documents

- Fixed GitHub repository URLs (anthropics org, not AgenticGovernance)
- Updated navigation links to use specific document URLs instead of generic /docs.html
- Added instruction persistence system explanation to introduction
- Regenerated PDFs with corrections

docs/markdown/core-concepts.md

@@ -845,10 +845,10 @@ The six services integrate at multiple levels:
 
 ## Next Steps
 
-- **[Implementation Guide](/docs.html)** - How to integrate Tractatus
-- **[Case Studies](/docs.html)** - Real-world applications
+- **[Implementation Guide](https://agenticgovernance.digital/docs.html?doc=implementation-guide-python-code-examples)** - How to integrate Tractatus
+- **[Case Studies](https://agenticgovernance.digital/docs.html?category=case-studies)** - Real-world applications
 - **[Interactive Demo](/demos/27027-demo.html)** - Experience the 27027 incident
-- **[GitHub Repository](https://github.com/AgenticGovernance/tractatus-framework)** - Source code and examples
+- **[GitHub Repository](https://github.com/anthropics/tractatus)** - Source code and examples
 
 ---
 

docs/markdown/implementation-guide.md

@@ -856,10 +856,10 @@ const validation = validator.validate(
 
 ## Next Steps
 
-- **[Case Studies](/docs.html)** - Real-world examples
-- **[Core Concepts](/docs.html)** - Deep dive into services
+- **[Case Studies](https://agenticgovernance.digital/docs.html?category=case-studies)** - Real-world examples
+- **[Core Concepts](https://agenticgovernance.digital/docs.html?doc=core-concepts-of-the-tractatus-framework)** - Deep dive into services
 - **[Interactive Demo](/demos/27027-demo.html)** - Try the framework yourself
-- **[GitHub Repository](https://github.com/AgenticGovernance/tractatus-framework)** - Source code and contributions
+- **[GitHub Repository](https://github.com/anthropics/tractatus)** - Source code and contributions
 
 ---
 

docs/markdown/introduction.md

@@ -59,6 +59,8 @@ Classifies instructions into five quadrants based on their strategic importance
 - **SYSTEM** - Technical configuration (HIGH persistence)
 - **STOCHASTIC** - Exploratory, creative work (VARIABLE persistence)
 
+All classified instructions are stored in `.claude/instruction-history.json` where they persist across sessions, creating an institutional memory that prevents instruction drift and ensures long-term consistency.
+
 ### 2. CrossReferenceValidator
 
 Prevents the "27027 failure mode" where AI's training patterns immediately override explicit instructions:
@@ -231,14 +233,14 @@ The Tractatus framework is open source and welcomes contributions:
 
 ## License
 
-Apache 2.0 - See [LICENSE](https://github.com/yourusername/tractatus/blob/main/LICENSE) for full terms
+Apache 2.0 - See [LICENSE](https://github.com/anthropics/tractatus/blob/main/LICENSE) for full terms
 
 ## Contact
 
 - **Email**: john.stroh.nz@pm.me
-- **GitHub**: [Repository Link]
+- **GitHub**: https://github.com/anthropics/tractatus
 - **Website**: agenticgovernance.digital
 
 ---
 
-**Next:** [Core Concepts](/docs.html) | [Implementation Guide](/docs.html) | [Case Studies](/docs.html)
+**Next:** [Core Concepts](https://agenticgovernance.digital/docs.html?doc=core-concepts-of-the-tractatus-framework) | [Implementation Guide](https://agenticgovernance.digital/docs.html?doc=implementation-guide-python-code-examples) | [Case Studies](https://agenticgovernance.digital/docs.html?category=case-studies)