Web app development and workflow is pretty much a messy exercise that has few standards. I am trying to document the messiness and suggest one way around it that smoothly scales from a small project to a large project without using yet another workflow layer (YAWL).
I am assuming that you are using tools such as node, grunt and bower. While it is possible to use other tools such as makefiles or generators such as lineman or brunch, the issues that bring such complexity to the workflow process are built into the very nature of web protocols and application deployment model. Unlike java, which has standardized packaging and deployment models, web apps can take on a wide variety of packaging and deployment models based on several factors such as organizational process ("this is the way we do it"), bandwidth/latency constraints, dev debugging needs as well as application model (client heavy, SPA or server heavy).
There is a lively ecosystems to help manage this complexity as ment