Projects & folders
A project is just a folder you have added to Atlas. The sidebar shows your projects and their real subfolders, so you are always working with your actual folders, with a bit of color, icons, and pinning layered on top.
Add one
Click the plus next to Folders and choose any folder. Atlas reads through it and adds it to the tree. Nothing is moved or copied.
Make it yours
Right-click a project to set a color and a custom icon, so a glance at the sidebar tells you what is what. You can also archive a project you are done with to tuck it away, rescan one to pick up files you added elsewhere, or open it in Explorer.
Pin the ones you live in
Right-click any folder and choose Add to Quick Access to pin it near the top of the sidebar, within reach no matter how deep it really sits.
Rearrange
Create subfolders, rename, and move folders straight from the right-click menu; Atlas makes the change on disk and keeps up. Removing a project from Atlas only takes it out of the app, never off your drive.