fix: resolve __SPECKIT_COMMAND_*__ refs in preset skill rendering (#2717)

The preset skill layer mirrors command templates into SKILL.md files but
only ran resolve_skill_placeholders(), leaving command cross-references as
raw __SPECKIT_COMMAND_<NAME>__ placeholders instead of rendering them as
/speckit-<cmd> the way CommandRegistrar.register_commands() does. As a
result, presets that override core commands under the agent skill layer
(e.g. Claude --ai-skills) leaked the raw tokens into SKILL.md.

Add a shared PresetManager._resolve_skill_command_refs() helper that maps
the agent's invoke separator to IntegrationBase.resolve_command_refs(), and
call it right after resolve_skill_placeholders() in every preset
skill-rendering path: _register_skills() (install), the _reconcile_skills()
override-restoration block, and both _unregister_skills() restore paths.
This mirrors register_commands() and addresses the path divergence flagged
in #1976.

Add regression tests covering the install and restore paths.

AI assistance: authored with Claude Code (Anthropic) — analysis, patch, and
tests. Verified via the existing pytest suite plus a manual CLI install and
remove cycle on a Claude --ai-skills project.

src/specify_cli/presets.py

@@ -28,6 +28,7 @@ from packaging import version as pkg_version
 from packaging.specifiers import SpecifierSet, InvalidSpecifier
 
 from .extensions import REINSTALL_COMMAND, ExtensionRegistry, normalize_priority
+from .integrations.base import IntegrationBase
 
 
 def _substitute_core_template(
@@ -1058,6 +1059,9 @@ class PresetManager:
                         body = registrar.resolve_skill_placeholders(
                             selected_ai, fm, body, self.project_root
                         )
+                        body = self._resolve_skill_command_refs(
+                            body, registrar, selected_ai
+                        )
                     fm_data = registrar.build_skill_frontmatter(
                         selected_ai if isinstance(selected_ai, str) else "",
                         skill_name, desc,
@@ -1134,6 +1138,23 @@ class PresetManager:
             title_name = title_name[len("speckit."):]
         return title_name.replace(".", " ").replace("-", " ").title()
 
+    @staticmethod
+    def _resolve_skill_command_refs(
+        body: str, registrar: "CommandRegistrar", selected_ai: str
+    ) -> str:
+        """Render ``__SPECKIT_COMMAND_*__`` tokens in a skill body as invocations.
+
+        Looks up the agent's invoke separator and rewrites each
+        ``__SPECKIT_COMMAND_<NAME>__`` placeholder into the matching
+        slash-command invocation — ``/speckit-<cmd>`` for a ``-`` separator,
+        ``/speckit.<cmd>`` for ``.`` — the same rendering the command layer
+        applies via ``CommandRegistrar.register_commands()``.
+        """
+        separator = registrar.AGENT_CONFIGS.get(selected_ai, {}).get(
+            "invoke_separator", "."
+        )
+        return IntegrationBase.resolve_command_refs(body, separator)
+
     def _build_extension_skill_restore_index(self) -> Dict[str, Dict[str, Any]]:
         """Index extension-backed skill restore data by skill directory name."""
         from .extensions import ExtensionManifest, ValidationError
@@ -1310,6 +1331,7 @@ class PresetManager:
             body = registrar.resolve_skill_placeholders(
                 selected_ai, frontmatter, body, self.project_root
             )
+            body = self._resolve_skill_command_refs(body, registrar, selected_ai)
 
             for target_skill_name in target_skill_names:
                 skill_subdir = skills_dir / target_skill_name
@@ -1402,6 +1424,9 @@ class PresetManager:
                     body = registrar.resolve_skill_placeholders(
                         selected_ai, frontmatter, body, self.project_root
                     )
+                    body = self._resolve_skill_command_refs(
+                        body, registrar, selected_ai
+                    )
 
                 original_desc = frontmatter.get("description", "")
                 enhanced_desc = original_desc or SKILL_DESCRIPTIONS.get(
@@ -1439,6 +1464,9 @@ class PresetManager:
                     body = registrar.resolve_skill_placeholders(
                         selected_ai, frontmatter, body, self.project_root
                     )
+                    body = self._resolve_skill_command_refs(
+                        body, registrar, selected_ai
+                    )
 
                 command_name = extension_restore["command_name"]
                 title_name = self._skill_title_from_command(command_name)

tests/test_presets.py

@@ -2346,6 +2346,62 @@ class TestPresetSkills:
         metadata = manager.registry.get("self-test")
         assert "speckit-specify" in metadata.get("registered_skills", [])
 
+    def test_register_skills_resolves_command_refs(self, project_dir, temp_dir):
+        """Preset skill overrides must resolve __SPECKIT_COMMAND_*__ tokens (issue #2717).
+
+        ``_register_skills()`` previously ran only ``resolve_skill_placeholders()``,
+        so command cross-references leaked into SKILL.md as raw placeholders
+        instead of rendering as ``/speckit-<cmd>`` like the command layer.
+        """
+        self._write_init_options(project_dir, ai="claude")
+        skills_dir = project_dir / ".claude" / "skills"
+        self._create_skill(skills_dir, "speckit-specify")
+
+        preset_dir = self._create_command_preset(
+            temp_dir,
+            "cmdref-install",
+            "speckit.specify",
+            "Override specify",
+            "Run `__SPECKIT_COMMAND_SPECIFY__` then `__SPECKIT_COMMAND_PLAN__`.\n",
+        )
+
+        manager = PresetManager(project_dir)
+        manager.install_from_directory(preset_dir, "0.1.5")
+
+        content = (skills_dir / "speckit-specify" / "SKILL.md").read_text()
+        assert "__SPECKIT_COMMAND_" not in content, "raw command token leaked into SKILL.md"
+        # Claude's invoke_separator is "-", so tokens render as /speckit-<cmd>.
+        assert "/speckit-specify" in content
+        assert "/speckit-plan" in content
+
+    def test_restore_skill_resolves_command_refs(self, project_dir, temp_dir):
+        """Skill restore on preset removal must also resolve command tokens (issue #2717)."""
+        self._write_init_options(project_dir, ai="claude")
+        skills_dir = project_dir / ".claude" / "skills"
+        self._create_skill(skills_dir, "speckit-specify")
+
+        core_cmds = project_dir / ".specify" / "templates" / "commands"
+        core_cmds.mkdir(parents=True, exist_ok=True)
+        (core_cmds / "specify.md").write_text(
+            "---\ndescription: Core specify\n---\n\n"
+            "Then run `__SPECKIT_COMMAND_PLAN__`.\n"
+        )
+
+        preset_dir = self._create_command_preset(
+            temp_dir,
+            "cmdref-restore",
+            "speckit.specify",
+            "Override specify",
+            "Override body\n",
+        )
+        manager = PresetManager(project_dir)
+        manager.install_from_directory(preset_dir, "0.1.5")
+        manager.remove("cmdref-restore")
+
+        content = (skills_dir / "speckit-specify" / "SKILL.md").read_text()
+        assert "__SPECKIT_COMMAND_" not in content, "raw command token leaked on restore"
+        assert "/speckit-plan" in content
+
     def test_core_command_override_skill_uses_preset_command_description(self, project_dir, temp_dir):
         """Preset skill overrides for core commands should keep preset frontmatter descriptions."""
         self._write_init_options(project_dir, ai="claude")