Right, your comment implies that you can't use e.g. Webstorm for non-JS development. You can, and it'll be a pretty darn good experience. Webstorm just happens to be optimized for web stuff, and there are other IDEs that are optimized for other things.

So the answer to, "what if my employer has a repo of language X and then a different repo of Y?" is: it's very likely not a problem, because the IDEs are not as specialized as you're clearly imagining them to be.