Can I manually add/update/delete a URL from a collection?

Yes. You can manually add/update/delete a document/URL through the admin console for an HTTP or File System collection.

To add a URL to your HTTP collection, enter the web address and click "Add/Update":

To delete a URL from your collection, enter the web address and click "Delete":

To see the status of a URL, click "Status":

To add a file to your File collection, enter the file name and click "Add/Update":

To learn about manually adding document in a HTTP collection read: Add Document for HTTP Collection