The sidebar is yours to arrange. You can set the order of notes and folders by hand, keep empty folders as structure, and collapse what you are not using. This article covers what you can change and the one current boundary.
Reordering by hand
Drag notes and folders to set their order in the sidebar. The order you set is saved with your vault, so the tree stays the way you arranged it. You can also drag a note into a folder to file it there.
One boundary: reordering keeps a folder within its current parent. You can sort folders among their siblings, but dragging does not re-nest a folder underneath a different folder. Notes can move between folders, and folders keep their place in the hierarchy.
Selecting several at once
A plain click opens a note and clears any selection. To act on more than one note, build a selection set: Cmd-click (Ctrl-click on Windows and Linux) toggles a note in or out of the set, and Shift-click selects the range from the last note you clicked. With a set in hand, the right-click menu offers the bulk actions — move the whole set into a folder, send it to Trash, or move it to the archive. See Acting on several notes at once.
Folder notes
A folder can have one note that stands in as its index — its “folder note”. Right-click a note in a folder and choose Set as folder note to mark it, or Remove as folder note to clear it; the marked note shows an index badge next to its title in the tree. Right-click the folder itself to open or create its folder note. See Folder notes.
Empty folders and loose notes
Empty folders are kept on purpose; if you make a folder to fill later, it stays. Notes do not have to live in a folder at all; loose notes at the top level are first-class, not an error state.
Collapsing
Collapse a folder to tuck its contents away while you work elsewhere; expand it to bring them back. Collapse state is a convenience for the current session and is not part of the saved order.
Views and the footer
Between the notes tree and the bottom of the sidebar sits the Views section, where your saved views live; open one to see its filtered set in a tab. See Saved views.
At the very bottom, the sidebar footer holds Trash and, alongside it, Archive. Archive is for notes you want out of the tree but not deleted; open the panel to see what is archived and restore a note from it. See Archiving notes.
Limits
The sidebar arranges how your notes are presented; it does not change what they are or where their content lives. Folder names and ordering live inside the encrypted vault; see How Myne protects your notes.