chore: Organize repo structure - move files to proper directories

- Python modules → cortex/
- Test files → tests/
- Shell scripts → scripts/
- Documentation → docs/
- Admin files → internal/ (gitignored)

Cleanup of 62 misplaced root files.

Author: Mike Morgan

.gitignore

@@ -157,3 +157,6 @@ htmlcov/
 *.yaml.bak
 /tmp/
 .env
+
+# Internal admin files (bounties, payments, etc.)
+internal/

bounties_owed.csv

@@ -0,0 +1,147 @@
+#!/bin/bash
+# Cortex Linux - Repo Cleanup Script
+# Run this once to organize the repo for public launch
+# Usage: cd ~/cortex && bash cortex-cleanup.sh
+
+set -e
+
+echo "🧹 CORTEX LINUX REPO CLEANUP"
+echo "============================"
+echo ""
+
+cd ~/cortex || { echo "❌ ~/cortex not found"; exit 1; }
+
+# Confirm we're in the right place
+if [ ! -f "README.md" ] || [ ! -d ".git" ]; then
+    echo "❌ Not in cortex repo root. Run from ~/cortex"
+    exit 1
+fi
+
+echo "📁 Current root files: $(ls *.py *.sh *.json *.csv *.md 2>/dev/null | wc -l | tr -d ' ')"
+echo ""
+
+# Step 1: Create directories if they don't exist
+echo "1️⃣  Creating directory structure..."
+mkdir -p cortex/modules
+mkdir -p tests
+mkdir -p scripts
+mkdir -p docs
+mkdir -p internal
+
+# Step 2: Move Python modules into cortex/
+echo "2️⃣  Moving Python modules to cortex/..."
+for file in context_memory.py dependency_resolver.py error_parser.py \
+            installation_history.py installation_verifier.py llm_router.py \
+            logging_system.py; do
+    if [ -f "$file" ]; then
+        mv "$file" cortex/ 2>/dev/null && echo "   ✓ $file → cortex/"
+    fi
+done
+
+# Step 3: Move test files into tests/
+echo "3️⃣  Moving test files to tests/..."
+for file in test_*.py; do
+    if [ -f "$file" ]; then
+        mv "$file" tests/ 2>/dev/null && echo "   ✓ $file → tests/"
+    fi
+done
+
+# Step 4: Move shell scripts into scripts/
+echo "4️⃣  Moving shell scripts to scripts/..."
+for file in *.sh; do
+    # Keep this cleanup script in root temporarily
+    if [ "$file" != "cortex-cleanup.sh" ] && [ -f "$file" ]; then
+        mv "$file" scripts/ 2>/dev/null && echo "   ✓ $file → scripts/"
+    fi
+done
+
+# Step 5: Move markdown docs to docs/ (except key root files)
+echo "5️⃣  Moving documentation to docs/..."
+for file in *.md; do
+    case "$file" in
+        README.md|CHANGELOG.md|LICENSE|Contributing.md)
+            echo "   ⊘ $file (keeping in root)"
+            ;;
+        *)
+            if [ -f "$file" ]; then
+                mv "$file" docs/ 2>/dev/null && echo "   ✓ $file → docs/"
+            fi
+            ;;
+    esac
+done
+
+# Step 6: Move internal/admin files and gitignore them
+echo "6️⃣  Moving internal files to internal/..."
+for file in bounties_owed.csv bounties_pending.json contributors.json \
+            issue_status.json payments_history.json pr_status.json; do
+    if [ -f "$file" ]; then
+        mv "$file" internal/ 2>/dev/null && echo "   ✓ $file → internal/"
+    fi
+done
+
+# Step 7: Delete duplicate/junk files
+echo "7️⃣  Removing duplicate files..."
+rm -f "README_DEPENDENCIES (1).md" 2>/dev/null && echo "   ✓ Removed README_DEPENDENCIES (1).md"
+rm -f "deploy_jesse_system (1).sh" 2>/dev/null && echo "   ✓ Removed deploy_jesse_system (1).sh"
+
+# Step 8: Update .gitignore
+echo "8️⃣  Updating .gitignore..."
+if ! grep -q "internal/" .gitignore 2>/dev/null; then
+    echo "" >> .gitignore
+    echo "# Internal admin files (bounties, payments, etc.)" >> .gitignore
+    echo "internal/" >> .gitignore
+    echo "   ✓ Added internal/ to .gitignore"
+else
+    echo "   ⊘ internal/ already in .gitignore"
+fi
+
+# Step 9: Create __init__.py files if missing
+echo "9️⃣  Ensuring Python packages are importable..."
+touch cortex/__init__.py 2>/dev/null
+touch tests/__init__.py 2>/dev/null
+echo "   ✓ __init__.py files created"
+
+# Step 10: Show results
+echo ""
+echo "📊 CLEANUP COMPLETE"
+echo "==================="
+echo "Root files now: $(ls *.py *.sh *.json *.csv 2>/dev/null | wc -l | tr -d ' ') (should be ~0)"
+echo ""
+echo "Directory structure:"
+echo "  cortex/     - $(ls cortex/*.py 2>/dev/null | wc -l | tr -d ' ') Python modules"
+echo "  tests/      - $(ls tests/*.py 2>/dev/null | wc -l | tr -d ' ') test files"
+echo "  scripts/    - $(ls scripts/*.sh 2>/dev/null | wc -l | tr -d ' ') shell scripts"
+echo "  docs/       - $(ls docs/*.md 2>/dev/null | wc -l | tr -d ' ') markdown files"
+echo "  internal/   - $(ls internal/ 2>/dev/null | wc -l | tr -d ' ') admin files (gitignored)"
+echo ""
+
+# Step 11: Git commit
+echo "🔟 Committing changes..."
+git add -A
+git status --short
+echo ""
+read -p "Commit and push these changes? (y/n): " -n 1 -r
+echo
+if [[ $REPLY =~ ^[Yy]$ ]]; then
+    git commit -m "Reorganize repo structure for public launch
+
+- Move Python modules to cortex/
+- Move tests to tests/
+- Move scripts to scripts/
+- Move docs to docs/
+- Move internal admin files to internal/ (gitignored)
+- Remove duplicate files
+- Clean root directory for professional appearance"
+    
+    git push origin main
+    echo ""
+    echo "✅ DONE! Repo is now clean and pushed."
+else
+    echo ""
+    echo "⚠️  Changes staged but NOT committed. Run 'git commit' when ready."
+fi
+
+echo ""
+echo "🧪 NEXT STEP: Test the CLI"
+echo "   cd ~/cortex && source venv/bin/activate && cortex install nginx --dry-run"
+echo ""