I just discovered that several packages are not installed in a window that was opened recently. Looks like all of my community packages were somehow uninstalled. I have another window open that apparently still has the packages loaded. For example, atom-beautify. If I search for atom-beautify in Settings > Installed Packages, it doesn’t appear. But when I go to Install Packages and search for it, its entry shows that it is installed.
What is the problem and how can I resolve it without having to reinstall all of my packages manually?