IDE-independence has a lot of advantages. Command-line only environments play nice with continuous build systems. They make it easier to on-board new developers by removing IDE-specific tweaks that often take root as undocumented lore. They tend to be more stable, more future-proof, and more popular than IDE-specific build techniques. (Which makes a big difference when you have to go ask a question on StackOverflow.) Also, developers have their favorite tools for a reason, and when you force them to use something else it hurts their productivity.
When starting a new software project you should adopt a strict IDE-agnostic policy. The rule is “I shouldn’t be able to tell from anything you check in to source control which IDE (if any) you are using”. Putting this policy into place isn’t hard–it’s just a matter of using the right tools to create a fresh project. After that, things pretty much take care of themselves. A little up-front standardization wards off a lot of build environment technical debt down the line.