By placing the file there in Explorer, Eclipse was not aware of its existence. Therefore, it never copied the .js file over to the deployed WAR. You need to inform Eclipse that the file is there. You can do it either the way you said (copy into Eclipse) or after copying via Explorer, hit F5 to refresh your project.
Moral of the story: if the file does not show up in the package view in Eclipse, the file does not exist within your project!
Your files, including CSS, must all be in the WebContent directory. Actually, they really just need to be in the deployed WAR file. So if you don't want to copy those files into your project,
you should look into using a build tool such as
Ant or Maven to build the WAR.