Making "web storm" optional, and then including the web storm -specific instructions in a "for web storm users" section. General instructions from the unix cli perspective. We don't all use web storm and its better in general to explain install/run without ref to any IDE. Most node users will be running from the cli
Indicate somewhere what has to be changed/added in the config files (as opposed to the web storm settings). It's easy enough to figure out when you look at them, but I think you should document it anyway.
Make it clear that the app WON'T build with node 0.10 (or alternatively use a diff encryption module)