Seems that in the latest WebStorm (2016.2.3?), node_modules is marked as an excluded directory by default. There are certain directories within node_modules that I want to include in my project files and searches. So I used to go to Preferences > Directories and exclude all of the modules I didn't need. However, I'm not able to "unexclude" the parent node_modules anymore. I have also tried unchecking the option in Preferences > Languages > JavaScript > Libraries without luck.
Same question with screenshot, if needed: Can't remove node_modules from excluded folders in WebStorm