deletes original files when pretending to delete only linked files (APPALLING)

[emmanueldufour]

Steps to reproduce

From a fresh installation and clean workspace:
create a java empty project
delete the "module-info.java" in the src folder
in package explorer :
-drag and drop a folder from the computer file system containing java files in the "SRC" folder of the project
-choose "link to files and folders", and "creater link locations relative to PROJECT_LOC"
-delete the packages you just created in the SRC folder, "delete these x elements" click OK, then on the confirmation box "Confirm Linked Folder Delete" it clearly says "Linked target will remain unchanged", click Yes, then confirm the "changes to be performed" and poof your linked files, I mean the real ones, not just the links are deleted......APPALLING

I expected: delete the links not the files

But got: deleted source files

## Tested under this environment:
* OS & version: win 11
* Eclipse IDE/Platform version (as shown in *Help > About*):
* Eclipse IDE for Enterprise Java and Web Developers
Version: 2025-09 (4.37.0)
Build id: 20250905-1456


## Community

- [ ] I understand reporting an issue to this OSS project does not mandate anyone to fix it. Other contributors may consider the issue, or not, at their own convenience. The most efficient way to get it fixed is that I fix it myself and contribute it back as a good quality patch to the project.

[HeikoKlare]

I tried to reproduce the issue following your instructions as exactly as possible, but for me everything works as expected:

delete_linked.mp4

I see different dialogs than what you seem to face according to your description (two dialogs for the deletion confirmation). @emmanueldufour can you check if I missed anything from your description or if anything was missing in the description? If not, can you please retest with the latest I-Build version of Eclipse? My test is done with the development state from yesterday.

[emmanueldufour]

https://github.com/user-attachments/assets/672be72a-e9d8-43f1-883f-1e7c8bdacdae
I confirm the disaster using the latest Integration build as shown

[HeikoKlare]

Thank you for sharing the video! I was now able to figure out the difference in our setups: you have a hierarchy of namespaces with the top-level package (the one only consisting of the first namespace com) not containing any classes. In consequence, the delete operation is executed on the packages actually containing classes (such as com.webcrawler), but that one is not linked itself (just its parent com is), which the operation command does not seem to properly deal with. When you put a (dummy) class in the com package, the problem disappears.

So the behavior is definitely seems to be a bug. I cannot estimate how often people chose to link their sources into the project, but in case one follows this approach, the issue might be quite severe for them as the class structure (i.e., not having a class in the top-level package) is completely common (mine in the first try to reproduce was just too simple). I guess that not many users link their sources into their projects (or if they do, they don't delete all the packages), which is why the bug that does not kick in that often and no one noticed (or reported) so far. Do you know if the behavior was ever correct or may it always have been like this?