Exclude folder from search but not from the project list

Question

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.

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.

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).

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.