I struggled quite some time with Closure Compiler, and in particular with CG's broken/inofficial support for CommonJS modules. I succeeded by pasting all module code into one file, removing `require()` calls and presenting only the single concatenated file to CG (and the minification and linting results were very good).

Granted, this is only possible if you reference modules/classes uniformly by the same name across your source, rather than using CommonJS "import as", and it only applies if you have no or few external dependencies which isn't realistic in the general case. Supposedly, using ES6 modules fixes this but I haven't checked yet.