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Extra warnings flags and resulting fixes on 31x

Andy Buckley requested to merge cms-ruleofthree-31 into release-3-1-x

Apply the CMS deprecated-copy and other extra warnings, and fix as many resulting issues as possible. Remaining unsquishable issues are in HepMC and FastJet and should be reported if not already done. Flag not applied by default as a result: kept in the --enable-extra-warnings flag, which we already had.

Not really necessary to do anything with this one, but it was a cleaner slate on which to test the effects before 3.2. If we need a 3.1.10 (sigh), this may as well be in it, so we can merge to the release branch and let's see what happens.

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