For the first, I think maintaining package-add instructions is table stakes, we need to be opinionated here. Agents are typically good at following them, if not you can fall over to a Makefile that does everything.

For the second, I totally agree. I continue to hope that agents will get better at refactoring, and I think using LSPs effectively would make this happen. Claude took dozens of minutes to perform a rename which Jetbrains would have executed perfectly in like five seconds. Its approach was to make a change, run the tests, do it again. Nuts.