fix: resolve database path inconsistency causing DB failures since v2.10.5

- Fix inconsistent database path in scripts/test-code-node-fixes.ts
  (was using './nodes.db' instead of './data/nodes.db')
- Remove incorrect database file from project root
- Ensure all scripts consistently use ./data/nodes.db as default path
- Resolves issues where rebuild creates database but MCP tools fail

Fixes database initialization problems reported by users since v2.10.5
where rebuild appeared successful but MCP functionality failed due to
incomplete database schema in root directory.

scripts/test-code-node-fixes.ts

@@ -10,7 +10,7 @@ import { getToolDocumentation } from '../src/mcp/tools-documentation';
 import { ExampleGenerator } from '../src/services/example-generator';
 import { EnhancedConfigValidator } from '../src/services/enhanced-config-validator';
 
-const dbPath = process.env.NODE_DB_PATH || './nodes.db';
+const dbPath = process.env.NODE_DB_PATH || './data/nodes.db';
 
 async function main() {
   console.log('🧪 Testing Code Node Documentation Fixes\n');