Tim Jenness, could you review most of this?
Most changes are trivial, and looking at commit messages should tell you which ones might not be. The changes in RawIngestTask and the assemblers are the ones that were the most hairy. It might make sense to look at obs_base and pipe_base first, and then daf_butler and resources, as it was the higher-level package typing that led to the need to update some of the annotations in the two lower-level packages.
Nate Lust, could you look at the changes in the QuantumGraph subpackage in pipe_base? They're confined to one commit that should be obvious (and if I linked via SHA1 it'd probably break due to rebasing at some point).
Codecov doesn't like most of these, but only very slightly.