Add, move, and remove a root
Roots are the main folders Notate is pointed at on a per workspace basis. You are able to manage them from the app.
Add a root
Open a folder from the Folders header in the sidebar (the add-existing-folder button) and pick a directory on your disk. That folder becomes a root in the current workspace. If the folder already contains markdown files, Notate reads them in place; if it is empty, it fills up as you write.
Adding a folder with a lot of files shows a progress indicator for files and folders as it reads them, and you can cancel partway through. You control which files are read with the ignore list in Settings → Files (see How Notate stores your files).
Move a root on disk
To move a root to a different location on disk, use the relocate option (right-click a root in the sidebar and choose Relocate on Disk) rather than dragging the folder in Finder or Explorer. Notate moves the files and updates where it looks for them in one step, so the root keeps working. Moving the folder yourself instead leaves Notate pointing at the old location (see Reconnect an unavailable folder).
Remove a root
Removing a root unmounts it: Notate stops tracking that folder and it disappears from the workspace, but the directory and every file in it stay on your disk. Nothing is deleted. Add the folder again later and your notes come right back. If the same root is in more than one workspace, removing it takes it out of only the current workspace and leaves it in the others.
Removing a root is not deleting your notes
Because a root is a pointer to a real directory, removing it only breaks the connection. To actually delete notes, delete them inside the app, which moves them to trash where they can be recovered.