This is a suggestion mainly for Ubuntu users.
My Atom configuration has become rather bloated with many packages. I was using project-viewer to create virtual projects to launch in tree-view Projects panel. The Atom native file manager … File Open File and File Open Folder – is less than ideal and opens Nautilus to select folders/files.
Since I use Krusader Dual Panel file manager (the equivalent in Windows is Total Commander) I created some UserActions in Krusader and this now allows Krusader to act as a front-end to Atom to manage what is loaded into tree-view. Now I do not need project-viewer although I am thinking about other uses for this package.
Basically, the suggestion is to explore how other tools might work with Atom in a tool chain. For example, do I need terminal emulators in Atom if I can trigger Yakuake Terminal Emulator.