fix: ensure POSIX-compliant newlines in generated files (#856)

- Add final newline check to YAML config generation
- Add final newline check to YAML manifest generation
- Add final newline check to agent .md file generation
- Ensures all text files end with \n per POSIX standard
- Fixes 'No newline at end of file' git warnings

tools/cli/lib/config.js

@@ -33,7 +33,9 @@ class Config {
     });
 
     await fs.ensureDir(path.dirname(configPath));
-    await fs.writeFile(configPath, yamlContent, 'utf8');
+    // Ensure POSIX-compliant final newline
+    const content = yamlContent.endsWith('\n') ? yamlContent : yamlContent + '\n';
+    await fs.writeFile(configPath, content, 'utf8');
   }
 
   /**

tools/cli/lib/yaml-format.js

@@ -64,7 +64,8 @@ async function formatYamlContent(content, filename) {
       noRefs: true,
       sortKeys: false, // Preserve key order
     });
-    return formatted;
+    // Ensure POSIX-compliant final newline
+    return formatted.endsWith('\n') ? formatted : formatted + '\n';
   } catch (error) {
     console.error(chalk.red(`❌ YAML syntax error in ${filename}:`), error.message);
     console.error(chalk.yellow(`💡 Try manually fixing the YAML structure first`));