The editor scripts source can be found in the package at the "editor/_source/" directory. It is "human readable" as well as commented. There are a lot of files there that are organized on groups.
To maximize loading and execution performance, the production distribution code in compressed on fewer and smaller files, as described on "Performance". These files can be found at the "editor/js/" directory.
It is possible to run the editor using the original scripts in the "_source" directory. It is usefull when developing or debugging the editor. It is quite easy to do that. Just go the "editor" directory and overwrite fckeditor.html with fckeditor.original.html (remember to backup the first one).
So, to start using again the "compressed" files, just recover the backup "fckeditor.html" file.
An application has been developed to make it easy to update the compressed file in the "js" directory. It is called "FCKeditor.Packager". You can find it in the "_packager" directory.
Further documentation (readme) is available in the "_packager" directory itself.