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After clearing IDE cache, noticed that the navigator window doesn't show .js file structure. It refreshes correctly for other files like .java or .html. If IDE is reopened, explorer starts showing the file structure correctly.
Reducing priority as this happens for a specific case, I noticed this when tried opening a unittest .js under html.knockout project. I don't see this issue when .js files from any javascript2.* modules are opened or if I create/open .js in a HTML5Application.