If your project truly depends on those things, they should be declared dependencies. Presumably you have some tool for injecting such things into a shell that the agent can use (I use nix for this). So if you run the agent from that shell, it has what it needs. If the shell doesn't have what it needs, that's a bug which the agent can fix by declaring new dependencies, but you have to relaunch the agent in the updated shell--so there's your opportunity to weigh in on whether the new resources are appropriate.

The benefits of being persnickety about precisely defined dependencies have outweighed the headaches since long before agents came on the scene. Agents have just made it even more important to do so, because if you let them fetch things all willy nilly like you'll have "works on my machine" problems at a much greater rate than was previously possible.

(I use nix for this) ... If the shell doesn't have what it needs, that's a bug which the agent can fix by declaring new dependencies

Few realize that computing and AI alignment were solved by nix years ago. As each nix user transcends towards enlightenment, they cut themselves off from all internet and human contact. Total ego death. Only nix remains.