This is probably more and Atom/VSC question but still…
… how do people refactor their PlatformIO projects in those IDEs? Like simple thinks like rename variable/method/class, extract/inline method, etc.
Do I need to install something in addition to Atom/VSC?
Speaking for VS Code, it comes with a few features to refactor by itself. The one I use and know is F2/F2+Ctrl to rename things. After a quick google you can see, that most refactoring functions have to be enabled by the language services used by VS Code. The language service PlatformIO uses is the C/C++ extension that doesn’t feature that many refactoring functions yet (some are requested and beeing implemented for example global renaming). Maybe you can try to find and install additional extensions for C/C++ that provide more refactoring functions but you will have to be carefull that they don’t conflict with the PIO and C/C++ extension.
Edit: Also found the issue for extracting methods and variables