… and it’s like the idea of a project being composed of things that don’t just exist in a particular folder is foreign somehow.
Since you are using Ubuntu 18.04 I can summarise what I use to bring together into an Atom tree-view (Project) files scattered throughout my Ubuntu 16.04 file system.
First I create a number of project folders in my $HOME directory.
Also I have a special folder I named $HOME/__LINKS and inside this I add symlinks to scattered folders and files.
Next I use Krusader as my external file manager and I can select any $HOME project folder to launch inside Atom tree-view by adding a UserAction. For example I have created in $HOME/__LINKS a www symlink pointing to my www folder in /var. I select this www symlink in Krusader and then go to topbar Useractions to select custom Atom action
Add folder/file/symlink as shown in image below. The www symlink expands in Atom tree-view to show entire www structure.
This workflow allows me to use Krusader as the orchestrator of what project(s) I load into Atom. In other words use a toolchain.
This external file manager loads symlinks and folder/files into Atom tree-view. In Atom tree-view be careful to note the difference between right click
Remove Project Folder and
Delete. I suggest experimenting with test symlinks which are backed up.
As another approach I have tried
project-viewer package which brings together multiple files and assets.