Zotero

To add folder to your library, right click the My Library tab on the left and select New Collection. Then name your folder.

To add references to a folder, drag and drop references from the library into the folder, or right click a reference and go to Add to Collection > select the folder. You can also create a subcollection by right clicking on a folder and selecting New Subcollection. 

You can organize references in multiple folders. This will not create a duplicate reference in your main My Library folder. 

When you click a reference in a folder and press the Delete button on your keyboard, this will remove the reference from the folder but will not delete the reference from your main library. You can also right click and Remove Item from Collection.

To delete a reference and remove it from your library all together, right click and select Move Item to Trash. Your items will remain in the trash unless you right click and Empty Trash. 

If you saved the same reference multiple times, you can automatically remove duplicate records. 

Go to your Zotero library > Duplicate Items in the menu on the left. 

Click on the reference (it will automatically select all duplicate references), then click on the Merge items button. Zotero will usually keep the reference with the most information and an attached PDF.

If you have a PDF attached to a reference, double click the reference in your library, or right click and select Open PDF. 

You can select the Highlight Text button in the middle of the PDF viewer to highlight a piece of text. 

You can also select the Add Note button to add a sticky note with a text field.  

If you want to remove a highlight or note, right click and select delete. 

Zotero will automatically save your highlights and notes.

In your library, you can also right click and Add Note to write more notes that appear under the reference in your library and in the right panel. In this section, you can also add links and references.