Is there any way to set environment variables when running a Node.js app using JetBrains' official Node plugin for WebStorm (and their other IDEs as well)?
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No, it's not possible from WebStorm, environment variables should be defined in your system.
UPDATE: in the new versions it's possible to set environment variables in the Run/Debug configuration.
It is actually possible Here is the official doc: http://www.jetbrains.com/webstorm/webhelp/run-debug-configuration-node-js.html
Here is my screenshot