test: add skills coexistence e2e coverage

tests/skills-coexistence.nix

@@ -0,0 +1,58 @@
+{ self, nixpkgs, system }:
+
+let
+  pkgs = import nixpkgs { inherit system; };
+  testSkill = builtins.path {
+    path = ./fixtures/custom-skill;
+    name = "hermes-test-custom-skill";
+  };
+in
+pkgs.testers.runNixOSTest {
+  name = "hermes-skills-coexistence";
+
+  nodes.machine = { ... }: {
+    imports = [ self.nixosModules.hermes-agent ];
+
+    services.hermes-agent = {
+      enable = true;
+      package = self.packages.${system}.hermes-agent;
+      skills = {
+        bundled.enable = false;
+        custom.repo-watch = {
+          category = "research";
+          source = testSkill;
+        };
+      };
+      documents = {
+        "SOUL.md" = "# SOUL.md\nTest soul\n";
+        "AGENTS.md" = "# AGENTS.md\nTest agents\n";
+        "USER.md" = "# USER.md\nTest user\n";
+      };
+      config = {
+        toolsets = [ "all" ];
+        model = {
+          default = "moonshotai/kimi-k2.5";
+          provider = "openrouter";
+        };
+      };
+    };
+
+    system.stateVersion = "25.05";
+  };
+
+  testScript = ''
+    machine.wait_for_unit("multi-user.target")
+
+    machine.succeed("test -f /var/lib/hermes/.hermes/skills/research/repo-watch/SKILL.md")
+    machine.succeed("grep -F 'research/repo-watch' /var/lib/hermes/.hermes/skills/.nix-managed-skills.json")
+
+    machine.succeed("mkdir -p /var/lib/hermes/.hermes/skills/manual-test")
+    machine.succeed("cat > /var/lib/hermes/.hermes/skills/manual-test/SKILL.md <<'EOF'\n---\nname: manual-test\ndescription: unmanaged test skill\n---\n\n# manual-test\nEOF")
+    machine.succeed("chown -R hermes:hermes /var/lib/hermes/.hermes/skills/manual-test")
+
+    machine.succeed("/run/current-system/activate")
+
+    machine.succeed("test -f /var/lib/hermes/.hermes/skills/research/repo-watch/SKILL.md")
+    machine.succeed("test -f /var/lib/hermes/.hermes/skills/manual-test/SKILL.md")
+  '';
+}