When user tries emptying the trash with linked files, DT will ask whether the linked files should be removed from DT only or from the external folder all together. DT will either remove the files’ links from future re-indexing or delete the external file in the finder.
IMHO, that here is a small problem. For users who uses DT as the primary project management tool (like me), sometime they just want to focus on what they need most by un-cluttering the indexed group. Sometime they may want DT to delete the files right away instead of going to the finder and do it again. But the empty trash command does not distinguish the two different needs for linked files within the trashcan. Deleting large amount of external files from within DT is uncommon, but deleting a few selected files permanently from within DT is perhaps common (I think).
I am just wondering if the right-click menu can have two options: “Move to Trash” and “Remove from External Folder”. The users can still recover the files from Mac’s trashcan if they regret their decision.
Disclaimer: this may be a naive suggestion roots from illogical workflow.