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I'm trying to rebuild ign-msgs1 so that it will be up to date.

There might be a way to get this to work, but I wouldn't recommend it. Proto 3's API is not backwards compatible with Proto 2 (for example, no more optional fields). You can install Proto 2 and 3 side-by-side. Since ign-msgs1 and gazebo9 depend on Proto 2, I recommend you install and use that.

there are macros in ign-msgs1 Utils.cmake which are defined by ign-cmake0 in IgnUtils.cmake

I don't see a Utils.cmake on ign-msgs1. All its cmake macros should be coming from ign-cmake0. What are the conflicting macros you're seeing?

I'm wondering if there's a way to make ign-msgs use its own macros instead of getting them stomped on by ign-cmake0

We created ign-cmake so it could hold macros to be reused by all other Ignition libraries. So it's expected that the macros are coming from that package.