When you add a file or a directories to the Project tab, it appears as a link. 
You can delete
the link on the Project tab without affecting the actual file or directory. 
When you delete a
file or directory from the Filesystems tab, the file is deleted from you system.

To remove a file or package from the Project tab:
====error next line: should read Click the Project tab...====
Click the Filesystems tab in the Explorer.
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Right-click the node of the linked file or directory, and choose Delete from 
the contextual
menu.

To permanently delete the file or package:
Click the Filesystems tab of the Explorer:
Right-click the node of the file or directory, and choose Delete from the 
contextual menu.