but it really exsist:
Does this still occur when you reload the window? Did you check the packages folder?
yes, reload window, and uninstall a package, all packages uninstall occur error like that, they still in .atom/.apm folder, but removed in .atom/packages.
Then they’re uninstalled. .apm/ is just a list of packages that gets stored locally. packages/ is what matters.
This is a known Issue. There is a fix for it in v1.9.x: