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Actually, this message is the one that comes up to tell you that the file has changed on disk, and do you want to overwrite the contents. It most often occurs when we pull changes down from our ClearCase server to our local systems behind Eclipse's back. But it happened to me after I refreshed my projects, rebuilt, re-exported the jars and when I hit Ctrl/F11 to launch CTRC, I got: "The file has been changed on the file system. Do you want to overwrite the changes?" In this context, I was confused because I wasn't sure which file it was talking about. I would like to see the message enhanced to show the file name, and also be more specific as to whether you mean to overwrite the contents on disk or in memory.
This message actually comes from the editor. Launching will save any dirty editors you have open. If the dirty editor is on an out of sync resource, you get the prompt. Agree it might be useful to have the file name in the message. Catalog: Editor.error.save.outofsync.message in EditorMessages.properties
3.0 candidate
Removing target milestone, no further action for 3.0.
Fixed in HEAD. Available in builds > N20061122-0010.