Update flake inputs, disktree and the herdr skill

Update flake inputs, disktree and the herdr skill nixpkgs and nixpkgs-agents move to 39ad350, home-manager to 6b88c12 and openspec to 9111a76. That takes herdr to 0.9.3, so the herdr skill moves to the v0.9.3 tag with it. disktree 0.10.1 -> 0.11.0. nixpkgs has since gained its own disktree, but it is Linux-only and refuses to evaluate on aarch64-darwin, so the local package stays and its header now says so. atuin stays on the local 18.23.0 package: nixpkgs now has rustc 1.98 but still ships atuin 18.21.0, which would be a downgrade.