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I've been using CKeditor on this website since I started writing here. But despite of customizing my CKEditor with Plugins to suit my needs (because I did not know what I wanted, it essentially meant adding every suggested plugin into the kitty), I uploaded the compiled tarball to my site. To my dismay, the configuration settings did not show the new plugins; rather, it did not show any of the plugins that were extra than a full installation. I am using Drupal 7 installation. I searched and searched and found out that every decent tutorial mentioned about a plugin.js file in each plugin folder.

Trusting CKEditor to make a good compilation, I presumed that there must be something new in this version of CKEditor and the tutorials were rather legacy and did not work. All my plugins had single files in them on the installation site and apparently, none of them worked. I tried tweaking the ckeditor.config.js file, by manually adding the names of extra plugins that I wanted to load, but none of them still worked. So, I separately downloaded a plugin source and voila! there was a config.js sitting right there. Somehow, either the script in CKEditor compiler was not running, or I was doing it wrong. I separately downloaded each one of them and unzipped in the plugins folder. So far, they seem to be working pretty well, without messing around with the ckeditor.config.js . They are visible as a checklist in the path Home » Administration » Configuration » Content authoring | Full Editor » Editor Appearance

Thus, it seems that there is some problem with CKEditor compiling the plugins for us with their Drag and Drop feature and it should be avoided.