Starting in 2.7 the WAB Builder will minify the main config.json when the app is saved. So notepad++ see that as one line. I don't use notepad++ much but I would look for a beautify-er plugin.
I don't know what you are exactly looking for, but if Notepad++ can't open it... perhaps it is a plug in that you need.
I will defer to Robert's suggestion since I am not from that realm of GIS