Doesn't support multiple project folders in one window

**OS: Windows 10
Atom ver: 1.2.0
Script ver: 3.0.2
Language type: Java (although I believe the problem is not language-specific)**

I was compiling java files from multiple projects. If I use "Add Project Folder" to add different projects in one single window, script will only recognize the project in which a file is compiled first. Any files from different projects will fail to be compiled because script considers them to be in the same folder as the first project.