Creating project with Git doesn't load files into project.

Hello, I want to do something extremely simple and am now extremely frustrated so I apologize if my tone is a little harsh.

On the command line its extremely easy to do what I want to do, which is checkout a repository using Git and start coding. IntelliJ is deciding that it doesn't want to show me my project. It asks me:

"Would you like to create an IntelliJ IDEA project for the sources you have checked out to [project name]."

So I say yes, then I select to Create project from existing sources. Now it's telling me that the sources for my project have been found and I see a selection of directories/files, its all of the JavaScript files and other nonsense such as the gitignore. Basically everything that is important isn't there, if I continue through the IDE loads up and shows only the selected directories/files from the prvious step, basically the IDE is ignoring my entire project and it makes editing nearly impossible. It's possible to use a tiny little menu up on the top to navigate through directories and select files to edit. I want all of my directories and files to appear in the Project view.

This is a PHP Yii app, I used PHPStorm in a trial and found it to be a very amazing app. I do more than PHP/web stuff though. I do Python, C, Lua and Shell and IntelliJ supports all of those so I bought that instead. It seems though that IntelliJ is just a lot more dumb than PHPStorm? So basically to sum it up my question is: How do I clone a Git repository? Because while IntelliJ is cloning, it's not in any way usable.

PS: I apologize if this is extremely obvious, I come from the Command Line/Vim where everything makes sense. I decided to use IntelliJ because of its extremely good linting features for JavaScript and PHP (mainly detecting typos in variables), a feature that is absent from Vim (Syntastic is the best linting library for Vim, but it is really bad for PHP).