I just wanted to know how the worklight folder is compiled and copied inside the wlapp file. I am referring to the worklight folder which consists of the cordova plugins folder, worklight.js, cordova_plugins.js, etc.
These files are used during build-time by the Worklight Build Engine. They are located in the TMPDIR of your OS. Since you're using OS X you can open Terminal and run the command open $TMPDIR/wlBuildResources
(> your-WL-version\jslibexpanded).
I am guessing you are asking this because you are thinking of altering these files pre-build time? You must not do that as it may generate a faulty application (it does not go only to the wlapp file but also to the generated native project of any mobile environment you may have added to your application).
These resources are also deleted and re-created on each launch of Eclipse (with Worklight Studio installed).
This will of course also void any support requests.
Since this is probably related to your other question about using the Ionic Keyboard Cordova plug-in, note that in the upcoming MobileFirst Platform Foundation 7.1 there is Cordova application support, enabling you to create either an iOS or Android application with MPF as a plug-in like any other, thus you can also leverage any Cordova plug-in that you would like. More on this, soon, once 7.1 is released.