Deprecate configure skills

src/ucode/cli.py

@@ -2976,7 +2976,7 @@ def configure_mcp(
         raise typer.Exit(130) from None
 
 
-@configure_app.command("skills")
+@configure_app.command("skills", deprecated=True)
 def configure_skills(
     location: Annotated[
         str | None,
@@ -3017,6 +3017,16 @@ def configure_skills(
     """
     try:
         locations = _parse_skill_locations(location)
+        if locations:
+            print_warning(
+                "`ucode configure skills` is deprecated. Use `ucode skill add` to download "
+                "skills or add MCP scopes, and `ucode skill remove --mcp` to remove MCP scopes."
+            )
+        else:
+            print_warning(
+                "`ucode configure skills` is deprecated, but its bare utility-tools-only setup "
+                "has no replacement yet and remains supported."
+            )
         # `--skill` absent -> None (whole schema); present (even empty) -> the
         # explicit subset, so `--skill ""` downloads nothing.
         selected_skills = (

tests/test_cli.py

@@ -1549,6 +1549,26 @@ def test_mcp_remove_forwards_agent_scope(self):
         remove.assert_called_once_with(agents={"claude", "codex"})
 
 
+class TestConfigureSkillsDeprecation:
+    def test_warns_and_keeps_legacy_dispatch(self):
+        with patch("ucode.cli.configure_skills_mcp_command") as configure:
+            result = runner.invoke(app, ["configure", "skills", "--location", "a.b", "--mcp"])
+
+        assert result.exit_code == 0, result.output
+        assert "deprecated" in _strip_ansi(result.output).lower()
+        configure.assert_called_once_with(["a.b"])
+
+    def test_bare_command_explains_that_utility_setup_remains_supported(self):
+        with patch("ucode.cli.configure_skills_mcp_command") as configure:
+            result = runner.invoke(app, ["configure", "skills"])
+
+        output = _strip_ansi(result.output).lower()
+        assert result.exit_code == 0, result.output
+        assert "utility-tools-only setup" in output
+        assert "remains supported" in output
+        configure.assert_called_once_with([])
+
+
 class TestManagedSkillsOnLaunch:
     """Managed skills are delivered by download only: the launch path downloads them and never
     registers them on the skills MCP connection (only a developer's own `skill add --mcp` schemas