You can get multiple output files, just use multiple assemblies
Remember that the code is designed to work with the Google Closure compiler, which not only reduces the number of files to 1 (which is more effective for downloading by the browser), but also removes huge redundancy in the code. It also ensures that files are downloaded in the correct order.
If you do not want to embed, you can set the :optimizations option to :none (compared to :whitespace :simple or :advanced ). This can help you get closer to making sure that you check the target directory for temporary files that may be what you are after.
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