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Does it throw an exception file not found when your run it? That might have something to do with the 'virtual' path your assets are stored. Those are not consistent on every platform.
Packaged files have /snapshot/ prefix in their paths (or C:\snapshot\ in Windows). If you used pkg /path/app.js command line, then __filename value will be likely /snapshot/path/app.js at run time. __dirname will be /snapshot/path as well.
Does it throw an exception file not found when your run it? That might have something to do with the 'virtual' path your assets are stored. Those are not consistent on every platform.
Possibly useful:
detecting assets
snapshot filesystem