When using delete inside file container, real file is deleted, there is a confirm dialog, but I think it's mostly used to add many files from different location and then copy or move them to a new locasion in the other panel. Real deletion is less needed than just removing the items from container, so I suggest to...
Add a new dialog when using delete inside file container:
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Select the operation you want to perform:
[Remove from container only]* [Delete from disk and remove from container]*
[ ] Never ask again
* these should be the buttons, first one should be focused by default.
Or different dialog:
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Remove item(s) from container.
[ ] Delete also item(s) from disk
[ ] Never ask again
EDIT: This would be very useful to easily and quickly remove item(s) from container.