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

.serena/memories/codebase_structure.md

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+# Codebase Structure
+
+## Directory Layout
+```
+smartdeno/
+├── ts/                           # Source code
+│   ├── index.ts                 # Main entry point (exports SmartDeno)
+│   ├── plugins.ts               # Dependency imports
+│   ├── paths.ts                 # Path configurations
+│   ├── classes.smartdeno.ts     # Main SmartDeno class
+│   ├── classes.denodownloader.ts # Deno download logic
+│   ├── classes.scriptserver.ts   # Script execution server
+│   ├── classes.denoexecution.ts  # Script execution wrapper
+│   └── 00_commitinfo_data.ts    # Commit metadata
+├── test/                         # Test files
+│   └── test.ts                  # Main test suite
+├── dist_ts/                      # Compiled output (gitignored)
+├── .nogit/                       # Temporary/debug files (gitignored)
+├── assets/                       # Static assets
+├── .gitea/                       # Gitea-specific configs
+├── .vscode/                      # VS Code settings
+├── .claude/                      # Claude Code settings
+├── .serena/                      # Serena agent settings
+├── package.json                  # Package manifest
+├── tsconfig.json                 # TypeScript config
+├── npmextra.json                 # Extended npm metadata
+├── readme.md                     # Main documentation
+└── readme.hints.md              # Development hints (currently empty)
+```
+
+## Core Classes
+
+### SmartDeno (ts/classes.smartdeno.ts)
+Main orchestrator class with methods:
+- `start(options)` - Initialize and download Deno if needed
+- `stop()` - Cleanup resources
+- `executeScript(scriptArg)` - Execute a Deno script
+
+### DenoDownloader (ts/classes.denodownloader.ts)
+Handles Deno binary download:
+- Fetches latest Deno release from GitHub
+- Platform detection (Linux, macOS, Windows)
+- Architecture detection (x64, arm64)
+- Downloads and extracts Deno binary
+
+### ScriptServer (ts/classes.scriptserver.ts)
+Internal server for script execution
+
+### DenoExecution (ts/classes.denoexecution.ts)
+Wraps individual script execution
+
+## Entry Point Flow
+1. User imports from `@push.rocks/smartdeno`
+2. `index.ts` exports `SmartDeno` class
+3. User creates instance: `new SmartDeno()`
+4. User calls `await smartDeno.start()` to initialize
+5. User calls `await smartDeno.executeScript(code)` to run Deno code
+
+## Dependencies Pattern
+All external dependencies are:
+1. Imported in `plugins.ts`
+2. Exported as namespace
+3. Used with full path (e.g., `plugins.smartfile.fs.readFile()`)