Thank you for reporting this issue. I've also encountered this case when
upgrading tomcat7 and I agree this is rather annoying.
However I'm not sure to know what should be done here. I was under the
impression this dialog was actually expected when a package updates a
modified configuration file. The Policy §10.7.3 states (about
configuration files handled by maintainer scripts):
"...it is the responsibility of the package maintainer to provide
maintainer scripts which correctly create, update and maintain the
file and remove it on purge. [...] These scripts must be idempotent
[...], must cope with all the variety of ways dpkg can call
maintainer scripts, must not overwrite or otherwise mangle the
user's configuration without asking"
So I'm tempted to think that asking if the file should be overwritten or
not is actually compliant with the policy.
What behavior would you expect in this situation? Ignoring the update?
Merging the changes? (ucf has a --three-way option to allow merging the
changes, I don't know if it would help here).
This is the maintainer address of Debian's Java team
debian-j...@lists.debian.org for discussions and questions.