Update MCP server package name; bundled skills support

docs/nixos-setup.md

@@ -164,7 +164,7 @@ directory setup, config generation, secrets, documents, and service lifecycle.
     # ── MCP Servers ────────────────────────────────────────────────────
     mcpServers.filesystem = {
       command = "npx";
-      args = [ "-y" "@anthropic/mcp-filesystem" "/data/workspace" ];
+      args = [ "-y" "@modelcontextprotocol/server-filesystem" "/data/workspace" ];
     };
 
     # ── Container options ──────────────────────────────────────────────

nix/checks.nix

@@ -51,6 +51,26 @@
           echo "ok" > $out/result
         '';
 
+        # Verify bundled skills are present in the package
+        bundled-skills = pkgs.runCommand "hermes-bundled-skills" { } ''
+          set -e
+          echo "=== Checking bundled skills ==="
+          test -d ${hermes-agent}/share/hermes-agent/skills || (echo "FAIL: skills directory missing"; exit 1)
+          echo "PASS: skills directory exists"
+
+          SKILL_COUNT=$(find ${hermes-agent}/share/hermes-agent/skills -name "SKILL.md" | wc -l)
+          test "$SKILL_COUNT" -gt 0 || (echo "FAIL: no SKILL.md files found in skills directory"; exit 1)
+          echo "PASS: $SKILL_COUNT bundled skills found"
+
+          grep -q "HERMES_BUNDLED_SKILLS" ${hermes-agent}/bin/hermes || \
+            (echo "FAIL: HERMES_BUNDLED_SKILLS not in wrapper"; exit 1)
+          echo "PASS: HERMES_BUNDLED_SKILLS set in wrapper"
+
+          echo "=== All bundled skills checks passed ==="
+          mkdir -p $out
+          echo "ok" > $out/result
+        '';
+
         # Verify HERMES_MANAGED guard works on all mutation commands
         managed-guard = pkgs.runCommand "hermes-managed-guard" { } ''
           set -e

nix/nixosModules.nix

@@ -424,9 +424,14 @@
             fi
 
             if [ "$NEED_CREATE" = "true" ]; then
+              # Resolve numeric UID/GID for container --user flag
+              HERMES_UID=$(${pkgs.coreutils}/bin/id -u ${cfg.user})
+              HERMES_GID=$(${pkgs.coreutils}/bin/id -g ${cfg.user})
+
               echo "Creating container..."
               ${containerBin} create \
                 --name ${containerName} \
+                --user "$HERMES_UID:$HERMES_GID" \
                 --network=host \
                 --volume /nix/store:/nix/store:ro \
                 --volume ${cfg.stateDir}:/data \

nix/packages.nix

@@ -6,6 +6,13 @@
         inherit (inputs) uv2nix pyproject-nix pyproject-build-systems;
       };
 
+      # Import bundled skills, excluding runtime caches
+      bundledSkills = pkgs.lib.cleanSourceWith {
+        src = ../skills;
+        filter = path: _type:
+          !(pkgs.lib.hasInfix "/index-cache/" path);
+      };
+
       runtimeDeps = with pkgs; [
         nodejs_20 ripgrep git openssh ffmpeg
       ];
@@ -23,16 +30,23 @@
         installPhase = ''
           runHook preInstall
 
+          # Copy bundled skills into share directory
+          mkdir -p $out/share/hermes-agent
+          cp -r ${bundledSkills} $out/share/hermes-agent/skills
+
           # Wrap entry points from the uv2nix venv
           mkdir -p $out/bin
           makeWrapper ${hermesVenv}/bin/hermes $out/bin/hermes \
-            --prefix PATH : "${runtimePath}"
+            --prefix PATH : "${runtimePath}" \
+            --set HERMES_BUNDLED_SKILLS $out/share/hermes-agent/skills
 
           makeWrapper ${hermesVenv}/bin/hermes-agent $out/bin/hermes-agent \
-            --prefix PATH : "${runtimePath}"
+            --prefix PATH : "${runtimePath}" \
+            --set HERMES_BUNDLED_SKILLS $out/share/hermes-agent/skills
 
           makeWrapper ${hermesVenv}/bin/hermes-acp $out/bin/hermes-acp \
-            --prefix PATH : "${runtimePath}"
+            --prefix PATH : "${runtimePath}" \
+            --set HERMES_BUNDLED_SKILLS $out/share/hermes-agent/skills
 
           runHook postInstall
         '';

tests/tools/test_skills_sync.py

@@ -4,6 +4,7 @@ from pathlib import Path
 from unittest.mock import patch
 
 from tools.skills_sync import (
+    _get_bundled_dir,
     _read_manifest,
     _write_manifest,
     _discover_bundled_skills,
@@ -467,3 +468,24 @@ class TestSyncSkills:
         new_bundled_hash = _dir_hash(bundled / "old-skill")
         assert manifest["old-skill"] == new_bundled_hash
         assert manifest["old-skill"] != old_hash
+
+
+class TestGetBundledDir:
+    def test_env_var_override(self, tmp_path, monkeypatch):
+        """HERMES_BUNDLED_SKILLS env var overrides the default path resolution."""
+        custom_dir = tmp_path / "custom_skills"
+        custom_dir.mkdir()
+        monkeypatch.setenv("HERMES_BUNDLED_SKILLS", str(custom_dir))
+        assert _get_bundled_dir() == custom_dir
+
+    def test_default_without_env_var(self, monkeypatch):
+        """Without the env var, falls back to relative path from __file__."""
+        monkeypatch.delenv("HERMES_BUNDLED_SKILLS", raising=False)
+        result = _get_bundled_dir()
+        assert result.name == "skills"
+
+    def test_env_var_empty_string_ignored(self, monkeypatch):
+        """Empty HERMES_BUNDLED_SKILLS should fall back to default."""
+        monkeypatch.setenv("HERMES_BUNDLED_SKILLS", "")
+        result = _get_bundled_dir()
+        assert result.name == "skills"

tools/skills_sync.py

@@ -37,7 +37,14 @@ MANIFEST_FILE = SKILLS_DIR / ".bundled_manifest"
 
 
 def _get_bundled_dir() -> Path:
-    """Locate the bundled skills/ directory in the repo."""
+    """Locate the bundled skills/ directory.
+
+    Checks HERMES_BUNDLED_SKILLS env var first (set by Nix wrapper),
+    then falls back to the relative path from this source file.
+    """
+    env_override = os.getenv("HERMES_BUNDLED_SKILLS")
+    if env_override:
+        return Path(env_override)
     return Path(__file__).parent.parent / "skills"