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Links, tags, and folders have different uses. Use links (notes) for ideas. Tags are best used as a saved search, and so can be used to track the status of type of notes. Folders are the most strict and hierarchical, but are still useful for collecting notes that should be manipulated (shared, backed up, protected, deleted, etc.) together. Folders are also useful for hiding away notes that do not require a lot of exposure; like daily notes and personnel files.
The PARA system divides notes into four categories based on actionability. Typically, those categories are represented as folders, though not necessarily.