diff --git a/flake.nix b/flake.nix
index 5d15287..828c89a 100644
--- a/flake.nix
+++ b/flake.nix
@@ -23,10 +23,16 @@
           default = self.packages.${system}.hermes-agent;
         };
 
-        checks = import ./checks.nix {
-          inherit pkgs;
-          inherit (self.packages.${system}) hermes-agent;
-        };
+        checks =
+          (import ./checks.nix {
+            inherit pkgs;
+            inherit (self.packages.${system}) hermes-agent;
+          })
+          // {
+            skills-coexistence = import ./tests/skills-coexistence.nix {
+              inherit self nixpkgs system;
+            };
+          };
 
         devShells.default = pkgs.mkShell {
           packages = [ self.packages.${system}.hermes-agent ];
diff --git a/module.nix b/module.nix
index c332a9c..df9e682 100644
--- a/module.nix
+++ b/module.nix
@@ -505,6 +505,13 @@ in
     system.activationScripts."hermes-agent-setup" = lib.stringAfter [ "users" ] ''
       set -euo pipefail
 
+      # Ensure required directories exist during activation (do not rely on tmpfiles ordering)
+      install -d -o ${cfg.user} -g ${cfg.group} -m 0750 ${cfg.stateDir}
+      install -d -o ${cfg.user} -g ${cfg.group} -m 0750 ${cfg.stateDir}/.hermes
+      install -d -o ${cfg.user} -g ${cfg.group} -m 0750 ${cfg.stateDir}/.hermes/skills
+      install -d -o ${cfg.user} -g ${cfg.group} -m 0750 ${cfg.workingDirectory}
+      install -d -o ${cfg.user} -g ${cfg.group} -m 0750 ${builtins.dirOf cfg.logPath}
+
       # Link config file
       install -o ${cfg.user} -g ${cfg.group} -m 0640 -D ${configFile} ${cfg.stateDir}/.hermes/cli-config.yaml
 
diff --git a/tests/fixtures/custom-skill/SKILL.md b/tests/fixtures/custom-skill/SKILL.md
new file mode 100644
index 0000000..c42e462
--- /dev/null
+++ b/tests/fixtures/custom-skill/SKILL.md
@@ -0,0 +1,8 @@
+---
+name: repo-watch
+description: Test custom skill for nix-hermes-agent module validation.
+---
+
+# repo-watch
+
+Test skill body.
diff --git a/tests/skills-coexistence.nix b/tests/skills-coexistence.nix
new file mode 100644
index 0000000..e7c9e1c
--- /dev/null
+++ b/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")
+  '';
+}