I outed myself as a big JetBrains a couple of times over and I am still madly in love with almost everything they do, despite them not paying me one cent for this endorsement! Heck, I even have to pay for their products, these ungrateful bastards! Still, they are the best and usually I am very happy with their products. But even they screw up sometimes.
Well, this is a wordy headline. But if you are running into this problem – like I did – you might search exactly for this and this is called effective seo or something. Here is the premise: You are using Vagrant, like any self-respecting developer would do and you also have soft spot for JetBrains products, i.e. PhpStorm, then you might want to start and stop vagrant directly from your beloved IDE. As you should! You paid good money to be spared from entering commands into a terminal.