Ignore node_modules in Webstorm when using navigation pop-up

In Webstorm 8, you need to also visit Settings > JavaScript > Libraries and disable Node.js core modules and node_modules. The directory exclusion will then work as before.

To exclude the directory from being searched via navigation pop-up, pick node_modules directory in Project view, then from mouse context menu:

Mark Directory As -> Excluded

Directory could be restored via Preferences->Directories->Excluded Folders settings