The JavaScript code of CKEditor is delivered as one main ckeditor.js
file where all the code has been compressed and merged. When you customize CKEditor and change its source code, it makes sense to use our package file generator to compress your own code.
The package file generator tool is called CKPackager and you can refer to the CKPackager — Compressing CKEditor article from CKEditor 3.x Developer's Guide to find all the information you need to compress your own customized code.