fix: Comprehensive repository restructure and audit fixes

[superninja-app]

🔧 Comprehensive Repository Restructure & Audit

Summary

Complete repository restructure migrating all files from VantisOS/ subdirectory to repository root, fixing CI/CD pipelines, version consistency, devcontainer, and cleaning up AI session artifacts.

Critical Fixes

🏗️ Structure Migration

• Migrated 1719 files from VantisOS/ subdirectory to repository root
• Eliminated duplicate directory structure entirely
• 25 workspace crate members now properly accessible at userspace/
• Cargo.lock present at root for reproducible builds

🔄 CI/CD Pipeline (Error Masking Removed)

• Rewrote ci.yml: proper cargo fmt, clippy, test, build
• Rewrote build.yml: real build verification with failure reporting
• Rewrote test.yml: actual test execution without suppression
• Removed ALL 2>/dev/null || echo "..." error masking from workflows
• Added cargo caching for faster CI runs

🐳 DevContainer Fix

• Added username/uid/gid to common-utils feature (fixes vscode user)
• Removed unavailable /dev/kvm device mount
• Removed broken vscode extensions volume mount
• Using rust:1.85-bookworm (stable)

📌 Version Consistency

• Unified version to 0.4.1 across: Cargo.toml, README.md, CITATION.cff, SECURITY.md, CHANGELOG.md
• Removed inflated version references (v1.0.0 through v1.5.0)
• Fixed placeholder badge IDs (Discord, YouTube)
• Removed non-existent links (vantis.os, podcast, forum)

🏷️ Tag Standardization

• Added v prefix to all 22 old tags (0.0.1→v0.0.1, etc.)
• Removed old non-prefixed tags from remote
• All tags now use consistent v*.*.* format

🧹 Cleanup

• Removed 17+ AI session summary files
• Moved 11 guide docs from root to docs/guides/
• Removed workspace artifacts (.agent_hooks/, summarized_conversations/)
• Removed binary artifacts (kernel.o, .backup files)
• Removed duplicate SECURITY.MD, release_notes.md, TODO.md
• Enhanced health_check.sh with workspace, version, and CI integrity checks

Files Changed

• 1780+ files restructured (renames from VantisOS/ to root)
• Net reduction: ~67,000 lines removed (duplicates, AI artifacts, inflated docs)

Testing

• All workspace members verified present with Cargo.toml
• CI workflows verified free of error masking
• Version consistency verified across all config files
• Health check script enhanced with new validation checks

[CLAassistant]

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