One way to achieve this is to create a linked folder that points to the location of your JavaScript project.
New > Folder > Advanced > Link to Alternate Location
Then go to the location of JSProj.
The disadvantage is that it is a link to the file system, not a link in the workspace. Theoretically, you just want to add a JavaScript project to the path of creating a Java project, but it looks like it only works when they are both Java projects (or maybe the same type).
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