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Problems with setup.exe updates when cygwin is running

I've just had a bunch of problems with cygwin, including but not limited to those experienced here:

As it turns out in the end, these have been down to running setup.exe with cygwin running and getting the mesage about needing to reboot. However, even after reboot the system has been broken: inodes listed as changed, cp saying that files were changed during copy, etc. This all seems to be down to the setup.exe run. After reverting everything to previous, the problem has gone away entirely. I suggest that setup.exe needs robusting, at the very least giving a strong warning on update BEFORE changing things if the files are in use.

A general message to close running programs before installing is used as a cop-out by lots of other programs and is usually overkill, and thus ignored. So it needs to be clear and specific, if it is to be effective.

Also, having used google to search the archives, the cygwin mailing list does seem to be pretty unhelpful on some of these issues as most enquiries from those not deeply steeped in the lore of cygwin get quoted the problem reporting FAQ rather than any attempt made to help them. Maybe I've been spoiled by the support I've received on other free forums and from commercial companies who don't tell their customers to push off.

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