New references imported or added to Mendeley are saved in the All Documents folder by default; however, you can choose a specific folder using the Add to: drop-down menu similar to how you would save to a specific folder on your computer, an external drive, etc.
Mendeley Reference Manger for Desktop provides enhanced features for working with PDFs.
For example, you can highlight, annotate, and add notes to documents; your notes are also searchable in the desktop application.
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