I understand your concern.

My installation had a separate cnf file in the conf.d directory with a
couple of personal settings affecting the mysqld, among them the old
slow-query variables.

This was done in order to have the my.cnf upgrade smoothly among time.

What happened is that mysql-server did not restart, probably throwing a
complain but without stopping (and upgrading from 14.04 to 16.04 means
2900 MB of stuff to download, running on an SSD you really don't even
notice what is passing on the screen!), the other packages complaining
about not being able to connect to the socket... not exactly a good hint
about the server being off. Only at the very end installation ended up
with 2 packages misconfigured...

I suggest instead of that behaviour to hang the upgrade in case mysql-
server is not restarting with a notification showing the offending
settings in order for the sysadmin to understand what is going wrong and
act before going on.

Hope this suggestion will be accepted

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  mysql fails to start after upgrade if previous defaults were

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