fix: resolve __SPECKIT_COMMAND_*__ refs in preset skill rendering (#2717) (#2718)

* 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.

* test: cover reconcile-override and extension restore command-ref paths (#2718 review)

Copilot review flagged that the install and core-template restore paths
gained regression tests, but the reconcile project-override branch and the
extension-backed restore branch were uncovered. Add focused tests for both:

- test_reconcile_override_skill_resolves_command_refs: a project override
  wins after preset removal; _reconcile_skills must render command refs.
- test_extension_restore_resolves_command_refs: a skill restored from an
  extension command body must also render command refs.

Both fail on main and pass with the fix in 8dd93c0.

Author: huy1010

src/specify_cli/presets.py

@@ -28,6 +28,7 @@
 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 @@ def _reconcile_skills(self, command_names: List[str]) -> None:
                         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 @@ def _skill_title_from_command(cmd_name: str) -> str:
             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 @@ def _register_skills(
             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 @@ def _unregister_skills(self, skill_names: List[str], preset_dir: Path) -> None:
                     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 @@ def _unregister_skills(self, skill_names: List[str], preset_dir: Path) -> None:
                     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 +2346,154 @@ def test_skill_overridden_on_preset_install(self, project_dir, temp_dir):
         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_reconcile_override_skill_resolves_command_refs(self, project_dir, temp_dir):
+        """Reconcile's project-override restore must resolve command tokens (issue #2717).
+
+        When a preset that overrode a command is removed and a project override
+        becomes the winning layer, ``_reconcile_skills`` rewrites the skill from
+        the override body — which must also render ``__SPECKIT_COMMAND_*__`` tokens.
+        """
+        self._write_init_options(project_dir, ai="claude")
+        skills_dir = project_dir / ".claude" / "skills"
+        self._create_skill(skills_dir, "speckit-specify")
+
+        # Project override wins once the preset is removed; its body carries a
+        # command cross-reference token. No core template exists for "specify",
+        # so the skill is restored exclusively via the reconcile override branch.
+        overrides_dir = project_dir / ".specify" / "templates" / "overrides"
+        overrides_dir.mkdir(parents=True, exist_ok=True)
+        (overrides_dir / "speckit.specify.md").write_text(
+            "---\ndescription: Override specify\n---\n\n"
+            "Then run `__SPECKIT_COMMAND_PLAN__`.\n"
+        )
+
+        preset_dir = self._create_command_preset(
+            temp_dir,
+            "cmdref-reconcile",
+            "speckit.specify",
+            "Preset specify",
+            "Preset body\n",
+        )
+        manager = PresetManager(project_dir)
+        manager.install_from_directory(preset_dir, "0.1.5")
+        manager.remove("cmdref-reconcile")
+
+        content = (skills_dir / "speckit-specify" / "SKILL.md").read_text()
+        assert "override:speckit.specify" in content, "skill should be restored from the project override"
+        assert "__SPECKIT_COMMAND_" not in content, "raw command token leaked on reconcile"
+        assert "/speckit-plan" in content
+
+    def test_extension_restore_resolves_command_refs(self, project_dir, temp_dir):
+        """Extension-backed skill restore must resolve command tokens (issue #2717).
+
+        When a preset override is removed and the skill is restored from an
+        extension command body, ``__SPECKIT_COMMAND_*__`` tokens in that body
+        must render as slash-command invocations like the core-template path.
+        """
+        self._write_init_options(project_dir, ai="claude")
+        skills_dir = project_dir / ".claude" / "skills"
+        self._create_skill(skills_dir, "speckit-fakeext-cmd", body="original extension skill")
+
+        extension_dir = project_dir / ".specify" / "extensions" / "fakeext"
+        (extension_dir / "commands").mkdir(parents=True, exist_ok=True)
+        (extension_dir / "commands" / "cmd.md").write_text(
+            "---\ndescription: Extension fakeext cmd\n---\n\n"
+            "Then run `__SPECKIT_COMMAND_PLAN__`.\n"
+        )
+        extension_manifest = {
+            "schema_version": "1.0",
+            "extension": {
+                "id": "fakeext",
+                "name": "Fake Extension",
+                "version": "1.0.0",
+                "description": "Test",
+            },
+            "requires": {"speckit_version": ">=0.1.0"},
+            "provides": {
+                "commands": [
+                    {
+                        "name": "speckit.fakeext.cmd",
+                        "file": "commands/cmd.md",
+                        "description": "Fake extension command",
+                    }
+                ]
+            },
+        }
+        with open(extension_dir / "extension.yml", "w") as f:
+            yaml.dump(extension_manifest, f)
+
+        preset_dir = self._create_command_preset(
+            temp_dir,
+            "cmdref-ext-restore",
+            "speckit.fakeext.cmd",
+            "Override fakeext cmd",
+            "Override body\n",
+        )
+        manager = PresetManager(project_dir)
+        manager.install_from_directory(preset_dir, "0.1.5")
+        manager.remove("cmdref-ext-restore")
+
+        content = (skills_dir / "speckit-fakeext-cmd" / "SKILL.md").read_text()
+        assert "source: extension:fakeext" in content, "skill should be restored from the extension"
+        assert "__SPECKIT_COMMAND_" not in content, "raw command token leaked on extension 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")