Stunnix JavaScript Obfuscator has powerfull GUI shell called Project Manager. It can generate command line scripts to build/rebuild/clean entire or part of your project. Also low-level command line interface is available. You can protect JavaScript in .js files, as well as in HTML, PHP, ASP.NET, JSP, WSH/WSC files too.
Blinged JSON Validator is a free app to validate JSON files with syntax highlighting, whitespace indentation, error messaging, and hotkeys.
