You can add a reference to a folder in the Description field of a JIRA issue or in a JIRA comment by entering the whole URL of it (the URL that you see in address bar when you have the folder's content displayed in Documents tab of the project).
This does not work for files though.
You could add a request for this in the Bitbucket repository of Documents (https://bitbucket.org/StonikByte/documents-add-on/issues?status=new&status=open) so we can consider it as an item for a next version.
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