feat(core): Add permission-controlled Deno execution, configurable script server port, improved downloader, dependency bumps and test updates

.serena/memories/code_style_and_conventions.md

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+# Code Style and Conventions
+
+## Naming Conventions
+- **Interfaces**: Prefix with `I` (e.g., `IDenoRelease`, `IAsset`)
+- **Types**: Prefix with `T` (not heavily used in this codebase)
+- **Classes**: PascalCase (e.g., `SmartDeno`, `DenoDownloader`)
+- **Files**: Lowercase, hyphenated (e.g., `classes.smartdeno.ts`, `classes.denodownloader.ts`)
+- **Methods/Properties**: camelCase
+
+## File Organization
+- **Source**: `ts/` directory
+- **Tests**: `test/` directory
+- **Compiled Output**: `dist_ts/` (excluded from git)
+- **Temporary Files**: `.nogit/` directory (excluded from git)
+
+## File Naming Patterns
+- Classes: `classes.<name>.ts` (e.g., `classes.smartdeno.ts`)
+- Entry point: `index.ts`
+- Plugin/dependency imports: `plugins.ts`
+- Path configurations: `paths.ts`
+
+## Import Patterns
+1. **All module dependencies** imported in `ts/plugins.ts`
+2. **References use full path**: `plugins.moduleName.className()`
+3. **Local imports** use `.js` extension (for ESM compatibility)
+
+Example from plugins.ts:
+```typescript
+import * as smartfile from '@push.rocks/smartfile';
+export { smartfile };
+```
+
+Usage:
+```typescript
+import * as plugins from './plugins.js';
+plugins.smartfile.fs.writeFile(...);
+```
+
+## Class Patterns
+- Private properties for internal state
+- Public async methods for API
+- Dependency injection where appropriate
+- JSDoc comments for public methods
+
+## Module Resolution
+- Always use `.js` extension in imports (even for `.ts` files)
+- This is required for ESM compatibility with NodeNext resolution