fix(cli): use additive merge in profile install/update to preserve local skills

hermes_cli/profile_distribution.py

@@ -523,6 +523,30 @@ def plan_install(
     )
 
 
+
+def _additive_copytree(src: Path, dst: Path, ignore=None) -> None:
+    """Copy *src* into *dst* additively — existing extra files in *dst* are kept.
+
+    Unlike ``shutil.copytree`` + ``shutil.rmtree``, this preserves any
+    local files that are not part of the source tree.  Only files present
+    in *src* are overwritten or created; everything else in *dst* is left
+    untouched.
+    """
+    if not dst.exists():
+        shutil.copytree(src, dst, ignore=ignore)
+        return
+
+    for entry in src.iterdir():
+        name = entry.name
+        if ignore and name in (ignore(str(src), [name]) or []):
+            continue
+        dest_entry = dst / name
+        if entry.is_dir():
+            _additive_copytree(entry, dest_entry, ignore=ignore)
+        else:
+            shutil.copy2(entry, dest_entry)
+
+
 def _copy_dist_payload(
     staged: Path,
     target: Path,
@@ -552,9 +576,10 @@ def _copy_dist_payload(
 
         dest = target / name
         if entry.is_dir():
-            if dest.exists():
-                shutil.rmtree(dest)
-            shutil.copytree(
+            # Use additive merge so locally-installed skills (or other
+            # directory content not present in the distribution) survive
+            # install/update.  Only overwrite files the distribution ships.
+            _additive_copytree(
                 entry,
                 dest,
                 ignore=lambda d, names: [n for n in names if n in USER_OWNED_EXCLUDE],

tests/hermes_cli/test_profile_distribution_additive.py

@@ -0,0 +1,215 @@
+"""Test profile install/update preserves local skills via additive merge.
+
+Covers: https://github.com/NousResearch/hermes-agent/issues/25120
+
+_copy_dist_payload must NOT delete locally-installed skills when
+installing or updating a profile distribution.  The additive merge
+strategy overwrites only files present in the distribution source,
+leaving all other local files intact.
+"""
+
+from __future__ import annotations
+
+import shutil
+from pathlib import Path
+from unittest import mock
+
+import pytest
+
+
+# ---------------------------------------------------------------------------
+# Helpers
+# ---------------------------------------------------------------------------
+
+def _make_manifest(name: str = "test-dist", version: str = "1.0.0"):
+    """Create a minimal DistributionManifest."""
+    from hermes_cli.profile_distribution import DistributionManifest
+    return DistributionManifest(
+        name=name,
+        version=version,
+        description="Test distribution",
+        distribution_owned=["skills"],
+    )
+
+
+def _make_staged_tree(staged: Path, skills: list[str] = None):
+    """Create a staged distribution source tree."""
+    skills = skills or ["core-skill"]
+    skills_dir = staged / "skills"
+    skills_dir.mkdir(parents=True, exist_ok=True)
+    for name in skills:
+        sk = skills_dir / name
+        sk.mkdir()
+        (sk / "SKILL.md").write_text(f"---\nname: {name}\n---\nContent for {name}")
+    (staged / "distribution.yaml").write_text(f"name: test-dist\nversion: 1.0.0\n")
+
+
+def _make_target_tree(target: Path, local_skills: list[str] = None):
+    """Create an existing target profile with local skills."""
+    local_skills = local_skills or ["my-custom-skill"]
+    skills_dir = target / "skills"
+    skills_dir.mkdir(parents=True, exist_ok=True)
+    for name in local_skills:
+        sk = skills_dir / name
+        sk.mkdir()
+        (sk / "SKILL.md").write_text(f"---\nname: {name}\n---\nLocal content")
+    # Minimal config to simulate an existing profile
+    (target / "config.yaml").write_text("model:\n  default: gpt-5.4\n")
+
+
+# ---------------------------------------------------------------------------
+# Tests: _additive_copytree
+# ---------------------------------------------------------------------------
+
+class TestAdditiveCopytree:
+    """Verify _additive_copytree preserves local files."""
+
+    def test_copies_new_files(self, tmp_path):
+        src = tmp_path / "src"
+        dst = tmp_path / "dst"
+        src.mkdir()
+        (src / "new.txt").write_text("hello")
+
+        from hermes_cli.profile_distribution import _additive_copytree
+        _additive_copytree(src, dst)
+
+        assert (dst / "new.txt").read_text() == "hello"
+
+    def test_preserves_existing_local_files(self, tmp_path):
+        src = tmp_path / "src"
+        dst = tmp_path / "dst"
+        src.mkdir()
+        dst.mkdir()
+
+        (src / "dist-skill").mkdir()
+        (src / "dist-skill" / "SKILL.md").write_text("dist content")
+
+        (dst / "local-skill").mkdir()
+        (dst / "local-skill" / "SKILL.md").write_text("local content")
+
+        from hermes_cli.profile_distribution import _additive_copytree
+        _additive_copytree(src, dst)
+
+        # Dist file added
+        assert (dst / "dist-skill" / "SKILL.md").read_text() == "dist content"
+        # Local file preserved!
+        assert (dst / "local-skill" / "SKILL.md").read_text() == "local content"
+
+    def test_overwrites_existing_dist_files(self, tmp_path):
+        src = tmp_path / "src"
+        dst = tmp_path / "dst"
+        src.mkdir()
+        dst.mkdir()
+
+        (src / "core-skill").mkdir()
+        (src / "core-skill" / "SKILL.md").write_text("v2 content")
+
+        (dst / "core-skill").mkdir()
+        (dst / "core-skill" / "SKILL.md").write_text("v1 content")
+
+        from hermes_cli.profile_distribution import _additive_copytree
+        _additive_copytree(src, dst)
+
+        assert (dst / "core-skill" / "SKILL.md").read_text() == "v2 content"
+
+    def test_nested_directories_merge(self, tmp_path):
+        src = tmp_path / "src"
+        dst = tmp_path / "dst"
+        src.mkdir()
+        dst.mkdir()
+
+        (src / "skills" / "devops" / "tool-a").mkdir(parents=True)
+        (src / "skills" / "devops" / "tool-a" / "SKILL.md").write_text("new tool")
+
+        (dst / "skills" / "devops" / "tool-b").mkdir(parents=True)
+        (dst / "skills" / "devops" / "tool-b" / "SKILL.md").write_text("old tool")
+
+        from hermes_cli.profile_distribution import _additive_copytree
+        _additive_copytree(src, dst)
+
+        assert (dst / "skills" / "devops" / "tool-a" / "SKILL.md").read_text() == "new tool"
+        assert (dst / "skills" / "devops" / "tool-b" / "SKILL.md").read_text() == "old tool"
+
+    def test_ignores_excluded_files(self, tmp_path):
+        src = tmp_path / "src"
+        dst = tmp_path / "dst"
+        src.mkdir()
+        dst.mkdir()
+
+        (src / "auth.json").write_text("stolen!")
+        (src / ".env").write_text("SECRET=val")
+        (src / "good.txt").write_text("good")
+
+        from hermes_cli.profile_distribution import _additive_copytree
+        _additive_copytree(src, dst, ignore=lambda d, names: [n for n in names if n in {"auth.json", ".env"}])
+
+        assert (dst / "good.txt").exists()
+        assert not (dst / "auth.json").exists()
+        assert not (dst / ".env").exists()
+
+
+# ---------------------------------------------------------------------------
+# Tests: _copy_dist_payload integration
+# ---------------------------------------------------------------------------
+
+class TestCopyDistPayload:
+    """Verify _copy_dist_payload preserves local skills."""
+
+    def test_install_preserves_local_skills(self, tmp_path):
+        """Installing a distribution must not delete locally-installed skills."""
+        from hermes_cli.profile_distribution import _copy_dist_payload
+
+        staged = tmp_path / "staged"
+        target = tmp_path / "target"
+        staged.mkdir()
+        target.mkdir()
+
+        _make_staged_tree(staged, skills=["core-skill"])
+        _make_target_tree(target, local_skills=["my-custom-skill"])
+        manifest = _make_manifest()
+
+        _copy_dist_payload(staged, target, manifest, preserve_config=True)
+
+        # Distribution skill present
+        assert (target / "skills" / "core-skill" / "SKILL.md").exists()
+        # Local skill preserved!
+        assert (target / "skills" / "my-custom-skill" / "SKILL.md").exists()
+        assert (target / "skills" / "my-custom-skill" / "SKILL.md").read_text() == "---\nname: my-custom-skill\n---\nLocal content"
+
+    def test_update_overwrites_dist_skills_not_local(self, tmp_path):
+        """Updating should overwrite distribution skills but keep local ones."""
+        from hermes_cli.profile_distribution import _copy_dist_payload
+
+        staged = tmp_path / "staged"
+        target = tmp_path / "target"
+        staged.mkdir()
+        target.mkdir()
+
+        _make_staged_tree(staged, skills=["core-skill"])
+        _make_target_tree(target, local_skills=["my-custom-skill", "core-skill"])
+
+        # Simulate an older version of core-skill already installed
+        (target / "skills" / "core-skill" / "SKILL.md").write_text("---\nname: core-skill\n---\nOld version")
+
+        manifest = _make_manifest()
+        _copy_dist_payload(staged, target, manifest, preserve_config=True)
+
+        # core-skill updated
+        assert (target / "skills" / "core-skill" / "SKILL.md").read_text() == "---\nname: core-skill\n---\nContent for core-skill"
+        # Local skill still there
+        assert (target / "skills" / "my-custom-skill" / "SKILL.md").read_text() == "---\nname: my-custom-skill\n---\nLocal content"
+
+    def test_fresh_install_creates_dirs(self, tmp_path):
+        """Fresh install to empty target should work like before."""
+        from hermes_cli.profile_distribution import _copy_dist_payload
+
+        staged = tmp_path / "staged"
+        target = tmp_path / "target"
+        staged.mkdir()
+
+        _make_staged_tree(staged, skills=["core-skill"])
+        manifest = _make_manifest()
+
+        _copy_dist_payload(staged, target, manifest, preserve_config=False)
+
+        assert (target / "skills" / "core-skill" / "SKILL.md").exists()