Is it possible to ignore searching the node_modules folder when using WebStorm\'s navigation pop-up window (Command + Shift + N>
To exclude node_modules folder from all projects (only created after that change) you can add this folder to list of standard folders to ignore.
On startup PHPStorm window click "Configure > Settings".
Then navigate to Build, Execution, Deployment > Deployment > Options.
P.s. Closing the current project is very important. If you do this settings with active project, this will affect only current project.