That's your first complaint, about refactoring. It has nothing to do with your second complaint about the project structure.

Also, Sublime doesn't do refactoring but VSCode totally does, given appropriate language server support which does exist for e.g. typescript. I have no problem believing that IntelliJ has more and fancier refactorings and code navigation features, but honestly I have never had a lot of use for anything more than rename, goto definition, find all references, and most importantly function/variable name completion, which all work great in VSCode.