feat: Major directory reorganization and cleanup

Reorganized project structure for better maintainability and reduced
disk usage by 95.9% (11 GB -> 451 MB).

Directory Reorganization (85% reduction in root files):
- Created docs/ with subdirectories (deployment, testing, database, etc.)
- Created infrastructure/vpn-configs/ for VPN scripts
- Moved 90+ files from root to organized locations
- Archived obsolete documentation (context system, offline mode, zombie debugging)
- Moved all test files to tests/ directory
- Root directory: 119 files -> 18 files

Disk Cleanup (10.55 GB recovered):
- Deleted Rust build artifacts: 9.6 GB (target/ directories)
- Deleted Python virtual environments: 161 MB (venv/ directories)
- Deleted Python cache: 50 KB (__pycache__/)

New Structure:
- docs/ - All documentation organized by category
- docs/archives/ - Obsolete but preserved documentation
- infrastructure/ - VPN configs and SSH setup
- tests/ - All test files consolidated
- logs/ - Ready for future logs

Benefits:
- Cleaner root directory (18 vs 119 files)
- Logical organization of documentation
- 95.9% disk space reduction
- Faster navigation and discovery
- Better portability (build artifacts excluded)

Build artifacts can be regenerated:
- Rust: cargo build --release (5-15 min per project)
- Python: pip install -r requirements.txt (2-3 min)

Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>

scripts/check_record_counts.py

@@ -0,0 +1,98 @@
+#!/usr/bin/env python3
+"""
+Check record counts in all ClaudeTools database tables
+"""
+import sys
+from sqlalchemy import create_engine, text, inspect
+
+# Database connection
+DATABASE_URL = "mysql+pymysql://claudetools:CT_e8fcd5a3952030a79ed6debae6c954ed@172.16.3.30:3306/claudetools?charset=utf8mb4"
+
+def get_table_counts():
+    """Get row counts for all tables"""
+    engine = create_engine(DATABASE_URL)
+
+    with engine.connect() as conn:
+        # Get all table names
+        inspector = inspect(engine)
+        tables = inspector.get_table_names()
+
+        print("=" * 70)
+        print("ClaudeTools Database Record Counts")
+        print("=" * 70)
+        print(f"Database: claudetools @ 172.16.3.30:3306")
+        print(f"Total Tables: {len(tables)}")
+        print("=" * 70)
+        print()
+
+        # Count rows in each table
+        counts = {}
+        total_records = 0
+
+        for table in sorted(tables):
+            result = conn.execute(text(f"SELECT COUNT(*) FROM `{table}`"))
+            count = result.scalar()
+            counts[table] = count
+            total_records += count
+
+        # Group by category
+        categories = {
+            'Core': ['machines', 'clients', 'projects', 'sessions', 'tags'],
+            'MSP Work': ['work_items', 'tasks', 'billable_time', 'work_item_files'],
+            'Infrastructure': ['sites', 'infrastructure', 'services', 'networks', 'firewall_rules', 'm365_tenants', 'm365_licenses'],
+            'Credentials': ['credentials', 'credential_audit_logs', 'security_incidents'],
+            'Context Recall': ['conversation_contexts', 'context_snippets', 'project_states', 'decision_logs'],
+            'Learning': ['command_runs', 'file_changes', 'problem_solutions', 'failure_patterns', 'environmental_insights'],
+            'Integrations': ['msp_integrations', 'backup_jobs', 'backup_reports'],
+            'Junction': ['session_tags', 'session_work_items', 'client_contacts', 'project_repositories']
+        }
+
+        # Print by category
+        for category, table_list in categories.items():
+            category_tables = [t for t in table_list if t in counts]
+            if not category_tables:
+                continue
+
+            print(f"{category}:")
+            print("-" * 70)
+            category_total = 0
+            for table in category_tables:
+                count = counts[table]
+                category_total += count
+                status = "[OK]" if count > 0 else " "
+                print(f"  {status} {table:.<50} {count:>10,}")
+            print(f"  {'Subtotal':.<50} {category_total:>10,}")
+            print()
+
+        # Print any uncategorized tables
+        all_categorized = set()
+        for table_list in categories.values():
+            all_categorized.update(table_list)
+
+        uncategorized = [t for t in counts.keys() if t not in all_categorized]
+        if uncategorized:
+            print("Other Tables:")
+            print("-" * 70)
+            for table in uncategorized:
+                count = counts[table]
+                status = "[OK]" if count > 0 else " "
+                print(f"  {status} {table:.<50} {count:>10,}")
+            print()
+
+        # Print summary
+        print("=" * 70)
+        print(f"TOTAL RECORDS: {total_records:,}")
+        print(f"Tables with data: {sum(1 for c in counts.values() if c > 0)}/{len(tables)}")
+        print("=" * 70)
+
+        return counts, total_records
+
+if __name__ == "__main__":
+    try:
+        counts, total = get_table_counts()
+        sys.exit(0)
+    except Exception as e:
+        print(f"ERROR: {e}", file=sys.stderr)
+        import traceback
+        traceback.print_exc()
+        sys.exit(1)