In the CodeKit settings, select Languages / JavaScript to change the default settings for processing JavaScript. (They can be overridden for each file in the project.)
Change the setting for the second processing step (labeled “Then:”) from “Concatenate + minifiy” to “Merge Imported Files”. For any script file already in the project, check to see if it already has separate settings that still differ from this new default value.
In this case, " *-ck.js " - files should only be created if the source file imports another for concatenation, but not for regular script files.
Alternatively, you can specify a different output path for the generated ck files in the CodeKit / JavaScript / Output Paths settings to prevent the generated files from cluttering the source directory.
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