I've found a bug in latest CVS:

1. select some text
2. unselect the text
3. press the middle mouse button (i.e. paste from clipboard)
4. quit from LyX
LyX will close the current buffer, and delete the temp. directory,
but the LyX window will remain open (and the lyx process doesn't exit)

Perhaps this bug is related to the new copy to X-clipboard feature?

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