I\'ve been struggling to set up my cordova plugin project. Mainly due the facts that:
Plugins need to be in a separate folder away from the main project
read this https://cordova.apache.org/docs/en/edge/guide_appdev_hooks_index.md.html
I use NetBeans IDE on Debian Jessie. (NetBeans is best IDE for me, use it for QT, PHP, and now Cordova. But it uses a lot of RAM.)
After I push build button, my shell script removes, installs and runs the newly built app in VirtualBox (using adb). I don't move plugins to other directory because I don't need it, but you can set your directory and manually put plugin, and then include plugin using a script.