Just another tiny bug:

If the data is in a "clean" state (so Save is not enabled), making an edit in the tree (e.g. renaming a note) does not make it "dirty" and the Save menu item and button are still not available.

This is by design - all editing done in the tree (renaming, expand/collapse/coloring etc.) are saved immediately.

The Save button is used to delay saving of documents that might be big. Imagine that you have a note, in which you store about 50Mb of pictures, what would happen if it would save after typing each character, while for the tree it's easy.