To be clear, this comment is about IDEs for common languages where they are a viable and general consideration as the topic is about IDEs as a whole. Platforms and/or languages where IDEs are commonly known as limited/awful, with no alternatives, are a moot point and not the root of the topic's points.
The points made and most of these comments are a joke. Basically bad practice and poor use of source control is being blamed on IDEs. Anyone with these problems (in modern times, old projects/approaches are products of their time) simply isn't a competent dev and/or never studied. I don't even recall any of these things being an issue in the first months of learning to code, 10 years ago.
To be a good programmer, don't learn from bad sources and don't be overly lazy to the point you develop bad habits. You can do all of that while still using an IDE. How you use the tools available is on you, not on the tools.
If a tool is so bad it enforces bad practice and has no way to avoid complicating workflow, find a better alternative. A tool is meant to streamline and improve workflow, not hinder it. I've never chosen to use an IDE that has enforced any of the issues being commented on, as if the only alternative is avoiding IDEs outright. I choose to use IDEs that are best-suited for the language I am using, are flexible and allow me to work how I like without convoluting my workflow. I also never commit IDE or user-specific files to a repository as that's just awful practice.
I'm also yet to read a complaint in comments here that claims to be a specific IDE forcing or creating problems that isn't actually about a company/team that has created a terrible dev ecosystem (or backing off an archaic one) for a project that they restricted and boxed into an IDE. Just because poor project management can make a project a nightmare to work with doesn't make the tools involved the problem.