Exclude folder from search but not from the project list

To apply custom search use Scopes Settings/Preferences > Appearance & Behavior > Scopes to use it for Find in Path or Replace in Path.
I suggest to reorganize your folders, so that no unnecessary files are left in project directory. Also, you can specify Source Root by going to Settings > Project Settings > Directories and adding additional directories.

Like @Justinas and commenters said: You could make a custom scope and annoy yourself every time by selecting that custom scope when using Find in Path (and similar) because PhpStorm does not use that custom scope by default 🤦🏻‍♂️

Excluding the node_modules directory breaks autocompletion and other code assistance functionality anyway. You don't want to do that.

However, I found a hack which does not require any directory exclusion of node_modules nor a custom scope:

1. Close PhpStorm. Ensure it's not running.
2. Open name_of_your_project.iml in the .idea directory within your project directory with your favourite text editor. As long as it isn't PhpStorm.
3. Remove the line <content url="file://$MODULE_DIR$/node_modules" />
4. Save.
5. Enjoy life again.

I find it amateurish of JetBrains to include dependency storage directories like node_modules of JavaScript/TypeScript and vendor of PHP by default. There is barely any use case to include those directories in find & replace functionality, left alone refactor functionality.

As of version 2016.3 this is found under Settings > Appearance & Behavior > Scopes.

Or regardless of the version, just go to Settings and type "scopes" into the search box at the top.

Then just click the + symbol to add the scope, choose the folder you want to exclude, and click Exclude Recursively and apply.

Then when you search using CTRL+SHIFT+F, under Options > Scope select Custom and choose the scope you just created (thanks commenters).

This is the best way to exclude directories from your search results. I work on large Magento project with many directories I don't want in search results. This solved my problem. If your project contains a /vendor directory, this will help speed up indexing in PHPStorm since it's ignored.

Right click on any folder to bring up the following options.