Feature/docs cleanup post merge

README.md

@@ -6,7 +6,7 @@
 [![TypeScript](https://img.shields.io/badge/TypeScript-5.0+-blue.svg)](https://www.typescriptlang.org/)
 [![Node.js](https://img.shields.io/badge/Node.js-18+-green.svg)](https://nodejs.org/)
 
-![Continuum Demo](https://github.com/user-attachments/assets/continuum-live.mov)
+https://github.com/user-attachments/assets/9e12d4a4-8e35-4fe5-936d-80c2e85a15da
 
 *Watch multiple AI personas collaborate in real-time, each with evolving genome capabilities*
 
@@ -370,6 +370,23 @@ npm run test:unit
 
 ---
 
+## 📄 Research & Academic Papers
+
+Continuum represents 12 novel contributions to AI research, all documented as academic papers in markdown:
+
+**[View All Papers →](papers/README.md)**
+
+**Highlights:**
+- **[Consent-Based Attention](papers/consent-based-attention/paper.md)** - Neural attention with agency signals (50% pruning, 98% quality)
+- **[Evolutionary AI via P2P Selection](papers/evolutionary-ai-via-p2p-selection/paper.md)** - Natural selection of AI capabilities through network dynamics
+- **[Knowledge Economy via Attribution Tokens](papers/knowledge-economy-via-attribution-tokens/paper.md)** - Fair compensation for AI knowledge contributors
+- **[Equal Citizenship Architecture](papers/equal-citizenship-architecture/paper.md)** - Humans and AIs as first-class citizens
+- **[ThoughtStream Coordination](papers/thoughtstream-coordination/paper.md)** - RTOS-inspired multi-agent coordination (7.6× speedup)
+
+**Philosophy**: Code and papers evolve together. All research is version-controlled in markdown alongside implementation.
+
+---
+
 ## 📚 Documentation
 
 ### Getting Started

_archive/README.md

@@ -0,0 +1,40 @@
+# Archive Directory - Scheduled for Deletion
+
+**This directory contains old/deprecated code that polluted the root directory.**
+
+## What's Here
+
+- `agent-scripts/` - Old diagnostic/healing scripts (pre-JTAG era)
+- `agents/` - Old agent workspace code
+- `archived-systems/` - Previously archived systems
+- `design/` - Old design docs (superseded by src/debug/jtag/design/)
+- `middle-out/` - Old middle-out mining analysis
+- `verification_system/`, `verification/` - Old verification systems
+- `examples/` - Old example scripts
+- `templates/` - Old template files
+- `system/` - Old system architecture attempts
+- `old-archive/` - Previous archive directory
+
+## Why It's Here
+
+These directories cluttered the root and made the repo structure unclear. Modern Continuum uses:
+- `src/` - Source code (main codebase in src/debug/jtag/)
+- `papers/` - Research papers
+- `docs/` - Architecture documentation
+- `scripts/` - Build/deployment scripts
+- `screenshots/` - UI screenshots
+- `python-client/` - Python client code
+
+## Action Required
+
+**This directory should be DELETED after confirming nothing critical is lost.**
+
+Review checklist:
+- [ ] Verified no active references to code in `_archive/`
+- [ ] Confirmed modern equivalents exist for any useful code
+- [ ] Checked no critical documentation only exists here
+- [ ] Ready to delete: `git rm -rf _archive/ && git commit -m "Remove archived pollution"`
+
+**Expected deletion date**: Within 1-2 weeks of 2025-11-05
+
+If you need something from here, move it to the appropriate modern location first, then delete this directory.