diff --git a/nanobot/apps/cli/service.py b/nanobot/apps/cli/service.py
index dedd83628..eef3f5ad4 100644
--- a/nanobot/apps/cli/service.py
+++ b/nanobot/apps/cli/service.py
@@ -219,7 +219,13 @@ def _safe_skill_name(name: str) -> str:
     return f"cli-app-{clean or 'app'}"
 
 
-def _skill_relative_path(name: str) -> str:
+def _legacy_skill_name(name: str) -> str:
+    """Return the workspace skill name emitted before Agent Plugins support."""
+    clean = _SAFE_NAME_RE.sub("-", name.lower()).strip("-")
+    return f"cli-app-{clean or 'app'}"
+
+
+def _plugin_skill_relative_path(name: str) -> str:
     skill_name = _safe_skill_name(name)
     return f"plugins/{skill_name}/skills/{skill_name}/SKILL.md"
 
@@ -622,7 +628,7 @@ class CliAppManager:
                     "name": installed_name,
                     "entry_point": entry_point,
                     "source": str(data.get("source") or ""),
-                    "skill": _skill_relative_path(installed_name),
+                    "skill": self.skill_relative_path(installed_name),
                     "tool": "run_cli_app",
                 }
             )
@@ -653,7 +659,16 @@ class CliAppManager:
         return self.workspace / "plugins" / skill_name / "skills" / skill_name / "SKILL.md"
 
     def _legacy_skill_path(self, name: str) -> Path:
-        return self.workspace / "skills" / _safe_skill_name(name) / "SKILL.md"
+        return self.workspace / "skills" / _legacy_skill_name(name) / "SKILL.md"
+
+    def _installed_skill_path(self, name: str) -> Path:
+        path = self._skill_path(name)
+        legacy_path = self._legacy_skill_path(name)
+        return legacy_path if not path.is_file() and legacy_path.is_file() else path
+
+    def skill_relative_path(self, name: str) -> str:
+        """Return the existing skill path, falling back to the canonical plugin path."""
+        return self._installed_skill_path(name).relative_to(self.workspace).as_posix()
 
     def _app_payload(
         self,
@@ -690,7 +705,7 @@ class CliAppManager:
             "status": status,
             "logo_url": logo_url,
             "brand_color": brand_color,
-            "skill_installed": self._skill_path(name).is_file(),
+            "skill_installed": self._installed_skill_path(name).is_file(),
             "manifest": self._manifest_payload(app, logo_url=logo_url, brand_color=brand_color),
         }
 
@@ -726,7 +741,7 @@ class CliAppManager:
         name = str(app["name"])
         entry_point = str(app.get("entry_point") or "")
         strategy = self._strategy(app)
-        skill_path = _skill_relative_path(name)
+        skill_path = _plugin_skill_relative_path(name)
         plugin_path = f"plugins/{_safe_skill_name(name)}"
         capabilities = [
             compact_dict({
diff --git a/nanobot/apps/cli/utils.py b/nanobot/apps/cli/utils.py
index f0d4a53ec..49e074476 100644
--- a/nanobot/apps/cli/utils.py
+++ b/nanobot/apps/cli/utils.py
@@ -29,6 +29,9 @@ def runtime_lines_for_request(
     """Return CLI App annotations from an immutable request snapshot."""
     structured = metadata.get("cli_apps") if isinstance(metadata, Mapping) else None
     if isinstance(structured, list):
+        from nanobot.apps.cli import CliAppManager
+
+        manager = CliAppManager(workspace=workspace)
         structured_items = cast(list[Any], structured)
         mentions = [
             cast(Mapping[str, Any], item) for item in structured_items
@@ -41,8 +44,7 @@ def runtime_lines_for_request(
                 f"@{str(item['name']).strip().lower()} "
                 f"(installed; tool=run_cli_app; "
                 f"entry_point={str(item.get('entry_point') or 'unknown')}; "
-                f"skill=plugins/cli-app-{str(item['name']).strip().lower()}/skills/"
-                f"cli-app-{str(item['name']).strip().lower()}/SKILL.md). "
+                f"skill={manager.skill_relative_path(str(item['name']))}). "
                 "Read the skill when useful, then run this app with `run_cli_app`; do not bypass it with shell."
                 for item in mentions
                 if str(item.get("name") or "").strip()
diff --git a/nanobot/session/manager.py b/nanobot/session/manager.py
index 8658f5f67..723067ba9 100644
--- a/nanobot/session/manager.py
+++ b/nanobot/session/manager.py
@@ -285,7 +285,7 @@ class Session:
                     )
                     cli_lines.append(
                         f"[CLI App Attachment: @{name}; tool=run_cli_app; entry_point={entry_point}; "
-                        f"skill=plugins/cli-app-{name}/skills/cli-app-{name}/SKILL.md]"
+                        f"skill=skills/cli-app-{name}/SKILL.md]"
                     )
                 if cli_lines:
                     breadcrumbs = "\n".join(cli_lines)
diff --git a/tests/agent/test_session_manager_history.py b/tests/agent/test_session_manager_history.py
index 54c7554c0..357bdc20b 100644
--- a/tests/agent/test_session_manager_history.py
+++ b/tests/agent/test_session_manager_history.py
@@ -491,8 +491,7 @@ def test_get_history_synthesizes_cli_app_attachment_breadcrumb():
         "content": (
             "please use @drawio\n"
             "[CLI App Attachment: @drawio; tool=run_cli_app; "
-            "entry_point=cli-anything-drawio; "
-            "skill=plugins/cli-app-drawio/skills/cli-app-drawio/SKILL.md]"
+            "entry_point=cli-anything-drawio; skill=skills/cli-app-drawio/SKILL.md]"
         ),
     }]
 
diff --git a/tests/cli_apps/test_service.py b/tests/cli_apps/test_service.py
index 87a5a7a43..dc9c9afbf 100644
--- a/tests/cli_apps/test_service.py
+++ b/tests/cli_apps/test_service.py
@@ -882,6 +882,34 @@ def test_mentioned_installed_apps_only_returns_installed_mentions(tmp_path: Path
     ]
 
 
+def test_legacy_underscored_skill_remains_visible_and_removable(tmp_path: Path) -> None:
+    manager = _manager(tmp_path)
+    legacy = manager.workspace / "skills" / "cli-app-unimol_tools" / "SKILL.md"
+    legacy.parent.mkdir(parents=True)
+    legacy.write_text(
+        "---\nname: cli-app-unimol_tools\ndescription: Legacy Uni-Mol app.\n---\n",
+        encoding="utf-8",
+    )
+    manager._save_installed(
+        {"unimol_tools": {"entry_point": "cli-anything-unimol-tools", "source": "harness"}}
+    )
+
+    app = {
+        "name": "unimol_tools",
+        "entry_point": "cli-anything-unimol-tools",
+        "install_cmd": "pip install cli-anything-unimol-tools",
+    }
+
+    assert manager._app_payload(app, manager._load_installed())["skill_installed"] is True
+    assert manager.mentioned_installed_apps("use @unimol_tools")[0]["skill"] == (
+        "skills/cli-app-unimol_tools/SKILL.md"
+    )
+
+    manager.remove_skill("unimol_tools")
+
+    assert not legacy.exists()
+
+
 def test_install_rejects_unknown_and_script_strategy(tmp_path: Path) -> None:
     manager = _manager(tmp_path)
     _seed_catalog(manager)
diff --git a/tests/cli_apps/test_utils.py b/tests/cli_apps/test_utils.py
index 183169cc9..f162b16db 100644
--- a/tests/cli_apps/test_utils.py
+++ b/tests/cli_apps/test_utils.py
@@ -62,3 +62,24 @@ def test_structured_cli_app_attachment_injects_runtime_metadata(tmp_path):
     assert "tool=run_cli_app" in joined
     assert "entry_point=cli-anything-zoom" in joined
     assert "skill=plugins/cli-app-zoom/skills/cli-app-zoom/SKILL.md" in joined
+
+
+def test_structured_cli_app_attachment_uses_existing_legacy_skill(tmp_path):
+    legacy = tmp_path / "skills" / "cli-app-unimol_tools" / "SKILL.md"
+    legacy.parent.mkdir(parents=True)
+    legacy.write_text("# Legacy Uni-Mol\n", encoding="utf-8")
+
+    lines = runtime_lines(
+        SimpleNamespace(
+            content="please use @unimol_tools",
+            metadata={
+                "cli_apps": [{
+                    "name": "unimol_tools",
+                    "entry_point": "cli-anything-unimol-tools",
+                }],
+            },
+        ),
+        tmp_path,
+    )
+
+    assert "skill=skills/cli-app-unimol_tools/SKILL.md" in "\n".join(lines)