The other day I pressed some shortcut while I was checking the left sidebar in PhpStorm and the IDE started deleting the WordPress site's htdocs folder I was working on. It was a local development copy so this didn't cause a site/server downtime at all.
I was pretty quick to cancel the operation, however, it took some time to restore the site to its previous state. Also .git files weren’t restored! I had several WordPress plugins which have several different repositories.
It turns out that PhpStorm/intelliJ IDEA won’t restore any ignored files/folders when you choose to undo a delete action. The JetBrains developers created this ticket and it’s quite possible that it applies to intelliJ IDEA and other IDEs by JetBrains as well.
To remove .git and .svn files from the ignored files and folders list click on the file type and press the delete key or the minus (-) icon above the list.
Windows/Linux: is configured via the File > Settings > Editor > File Types
tab: Ignored Files and Folders"
Mac: Preferences > Editor > File Types > tab: Ignored Files and Folders
Here's a video how to remove files and folders from the exclude list
youtube video (with nice background music) - https://youtu.be/YWRd369Eg7U
Why is it important to configure PhpStorm’s ignore file and folder list?
You’re developing a site or an app, you are most likely using some sort of version control system to manage the code, coordinate your and/or your developers’ work. Git is usually a pretty good choice.
Maybe you’ve been working on a WordPress theme or WordPress plugin that’s in version control and accidentally deleted it. PhpStorm won't fully restore it. You’ll have to clone the project/folder again and restore it that way.
I’ve tried replacing the .git folder only but that caused issues. The IDE got confused and wasn’t pulling/pushing things correctly. Maybe I should have cleared the IDE cache.