Archive bootstrap investigation docs and update to v0.4.1

docs/ISSUE_REPORT.md

@@ -1,7 +1,7 @@
 # EigenScript Issue Report
 
-**Generated:** 2025-11-24  
-**Version:** 0.3.0  
+**Generated:** 2025-12-05
+**Version:** 0.4.1
 **Reporter:** GitHub Copilot Code Review Agent
 
 ---

docs/KNOWN_ISSUES.md

@@ -1,8 +1,8 @@
 # Known Issues - HONEST ASSESSMENT
 
-**Last Updated**: 2025-11-24
+**Last Updated**: 2025-12-05
 **Assessed By**: GitHub Copilot + automated analysis
-**Project Status**: **Beta 0.3** (Production-Ready Core, Polish Needed)
+**Project Status**: **v0.4.1** (Fixpoint Bootstrap Achieved)
 **Test Suite**: 665 passing, 0 failing ✅
 **Code Coverage**: 78% overall ✅
 **Example Success Rate**: 100% (30/30 working) ✅

docs/archive/bootstrap-investigation/README.md

@@ -0,0 +1,38 @@
+# Bootstrap Investigation Archive
+
+**Status: RESOLVED** (December 5, 2025)
+
+This directory contains historical documentation from the bootstrap investigation conducted December 3-5, 2025. These files document the debugging process that led to achieving **fixpoint bootstrap** in v0.4.1.
+
+## What Happened
+
+1. **Dec 3-4**: Investigation began into why Stage 1 compiler produced incorrect output
+2. **Dec 4-5**: Root causes identified and fixed:
+   - External variable assignment in codegen
+   - Runtime pointer detection for non-PIE binaries
+   - Cross-module global naming alignment
+3. **Dec 5**: Fixpoint bootstrap achieved - Stage 2 = Stage 3
+
+## Files in This Archive
+
+| File | Description |
+|------|-------------|
+| `BOOTSTRAP_PLAN_SUMMARY.md` | High-level investigation strategy |
+| `BOOTSTRAP_FIX_PLAN.md` | Detailed technical analysis of the numeric literal bug |
+| `BOOTSTRAP_INVESTIGATION_CHECKLIST.md` | Step-by-step debugging checklist |
+| `BOOTSTRAP_ROADMAP.md` | Phased approach to fixing bootstrap |
+| `BOOTSTRAP_DEBUG_QUICKREF.md` | Quick reference for debugging |
+| `BOOTSTRAP_INDEX.md` | Index of all bootstrap documentation |
+
+## Current Documentation
+
+For up-to-date information on the self-hosted compiler, see:
+- [SELF_HOSTING_QUICKSTART.md](../../SELF_HOSTING_QUICKSTART.md) - Get started in 5 minutes
+- [COMPILER_SELF_HOSTING.md](../../COMPILER_SELF_HOSTING.md) - Complete technical guide
+
+## Why Keep These Files?
+
+These documents are preserved for:
+1. **Historical reference** - Understanding the bootstrap journey
+2. **Learning** - Future debugging of similar issues
+3. **Attribution** - Recording the work that achieved this milestone

docs/index.md

@@ -3,7 +3,7 @@
 **A geometric programming language modeling computation as flow in semantic spacetime**
 
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
-[![Version](https://img.shields.io/badge/version-0.4.0-blue.svg)](https://github.com/InauguralSystems/EigenScript)
+[![Version](https://img.shields.io/badge/version-0.4.1-blue.svg)](https://github.com/InauguralSystems/EigenScript)
 
 ## What is EigenScript?