Stunnix Obfuscator Project Manager allows protection of projects of any complexity consisting of files of any type and potentially including code of any type (client-side, server-side, .asp pages with both server side and client-side code, .html files with client-side code). Different files can be processed with different sets of options or not processed at all. It has 'build project' functionality available in most popular IDEs which will result in processing only the files which are newer than the protected version. Files free from code (like images or .css files) will simply be copied to the directory with protected version of the project, allowing Project Manager to be used as a generic replacement for 'Make'-like utility. It completely eliminates the need to compose and invoke commands from the command line. All operations can be performed using mouse.

Users who prefer to use the command line will be able to compose a build script (a special project-specific perl program that effectively is a smart stand-alone replacement for project-specific Makefile that already includes functionality of the Make utility) for a project using Project Manager. That build script can then be invoked to perform desired operation like cleaning all output files, rebuilding only changed files or rebuilding all files (with ability to specify only a subset of files to be subject of an operation).