Fix extension skill command reference rendering

extensions/EXTENSION-USER-GUIDE.md

@@ -202,6 +202,16 @@ Jira Integration (v1.0.0)
 
 When an extension is removed, its corresponding skills are also cleaned up automatically. Pre-existing skills that were manually customized are never overwritten.
 
+When one extension command needs to reference another Spec Kit command, prefer the
+portable command token form, such as `__SPECKIT_COMMAND_PLAN__`, instead of
+hard-coding a slash command. Spec Kit renders these tokens to the active
+integration's command style. For skills-based integrations, generated extension
+skills also normalize literal slash-dot command references such as
+`/speckit.jira.specstoissues` to the active skill invocation form, for example
+`$speckit-jira-specstoissues` for Codex or `/speckit-jira-specstoissues` for
+slash-skills agents. Avoid using bare prose like `speckit.jira.specstoissues`
+when you intend the agent to invoke a command.
+
 ---
 
 ## Using Extensions

src/specify_cli/extensions/__init__.py

@@ -1562,7 +1562,6 @@ def _register_extension_skills(
         from .. import load_init_options
         from ..agents import CommandRegistrar
         from ..integrations import get_integration
-        from ..integrations.base import IntegrationBase
 
         written: List[str] = []
         opts = load_init_options(self.project_root)
@@ -1576,29 +1575,62 @@ def _register_extension_skills(
         integration = get_integration(selected_ai)
         ai_skills_enabled = is_ai_skills_enabled(opts)
 
+        def _render_skill_command_invocation(command_name: str) -> str:
+            """Render a command name with the active skill invocation style."""
+
+            if is_dollar_skills_agent(selected_ai, ai_skills_enabled):
+                return "$" + command_name.replace("speckit.", "speckit-").replace(
+                    ".", "-"
+                )
+            if is_slash_skills_agent(selected_ai, ai_skills_enabled):
+                return "/" + command_name.replace("speckit.", "speckit-").replace(
+                    ".", "-"
+                )
+            if integration is not None:
+                return integration.build_command_invocation(command_name)
+
+            separator = agent_config.get("invoke_separator", ".")
+            if not isinstance(separator, str) or not separator:
+                separator = "."
+            return "/" + command_name.replace(".", separator)
+
         def _resolve_command_ref_tokens(body: str) -> str:
             """Resolve explicit command-ref tokens with the active skill style."""
 
             def _replacement(match: re.Match[str]) -> str:
                 command_name = "speckit." + match.group(1).lower().replace("_", ".")
-                if is_dollar_skills_agent(selected_ai, ai_skills_enabled):
-                    return "$" + command_name.replace("speckit.", "speckit-").replace(
-                        ".", "-"
-                    )
-                if is_slash_skills_agent(selected_ai, ai_skills_enabled):
-                    return "/" + command_name.replace("speckit.", "speckit-").replace(
-                        ".", "-"
-                    )
-                if integration is not None:
-                    return integration.build_command_invocation(command_name)
-                return IntegrationBase.resolve_command_refs(
-                    match.group(0), agent_config.get("invoke_separator", ".")
-                )
+                return _render_skill_command_invocation(command_name)
 
             return re.sub(
                 r"__SPECKIT_COMMAND_([A-Z][A-Z0-9_]*)__", _replacement, body
             )
 
+        def _normalize_literal_slash_command_refs(body: str) -> str:
+            """Normalize literal /speckit.foo refs in generated skill bodies."""
+
+            def _replacement(match: re.Match[str]) -> str:
+                command_name = match.group("command")
+                if command_name.rsplit(".", 1)[-1] in {
+                    "json",
+                    "md",
+                    "toml",
+                    "txt",
+                    "yaml",
+                    "yml",
+                }:
+                    return match.group(0)
+                return _render_skill_command_invocation(command_name)
+
+            return re.sub(
+                (
+                    r"(?<![\w$:/-])"
+                    r"/(?P<command>speckit\.[A-Za-z0-9_-]+(?:\.[A-Za-z0-9_-]+)+)"
+                    r"(?![A-Za-z0-9_.-])"
+                ),
+                _replacement,
+                body,
+            )
+
         for cmd_info in manifest.commands:
             cmd_name = cmd_info["name"]
             cmd_file_rel = cmd_info["file"]
@@ -1678,6 +1710,7 @@ def _replacement(match: re.Match[str]) -> str:
                 selected_ai, frontmatter, body, self.project_root, extension_id=manifest.id
             )
             body = _resolve_command_ref_tokens(body)
+            body = _normalize_literal_slash_command_refs(body)
 
             original_desc = frontmatter.get("description", "")
             description = original_desc or f"Extension command: {cmd_name}"

tests/test_extension_skills.py

@@ -1166,12 +1166,24 @@ def test_skill_registration_resolves_command_ref_tokens(
         assert "__SPECKIT_COMMAND_PLAN__" not in content
         assert expected_invocation in content
 
-    def test_skill_registration_does_not_rewrite_literal_speckit_text(
-        self, project_dir, temp_dir
+    @pytest.mark.parametrize(
+        ("ai", "expected_invocation"),
+        [
+            ("claude", "/speckit-foo-bar"),
+            ("copilot", "/speckit-foo-bar"),
+            ("codex", "$speckit-foo-bar"),
+            ("command-code", "$speckit-foo-bar"),
+            ("kimi", "/skill:speckit-foo-bar"),
+            ("zcode", "$speckit-foo-bar"),
+            ("bob", "/speckit-foo-bar"),
+        ],
+    )
+    def test_skill_registration_rewrites_literal_slash_command_refs(
+        self, project_dir, temp_dir, ai, expected_invocation
     ):
-        """Auto-registered skills should leave literal speckit text untouched."""
-        _create_init_options(project_dir, ai="codex", ai_skills=True)
-        skills_dir = _create_skills_dir(project_dir, ai="codex")
+        """Auto-registered skills should normalize literal slash-dot refs."""
+        _create_init_options(project_dir, ai=ai, ai_skills=True)
+        skills_dir = _create_skills_dir(project_dir, ai=ai)
 
         ext_dir = temp_dir / "literal-ref-ext"
         ext_dir.mkdir()
@@ -1202,20 +1214,27 @@ def test_skill_registration_does_not_rewrite_literal_speckit_text(
             "---\n"
             "description: Run command\n"
             "---\n\n"
-            "Literal slash form: /speckit.foo.bar\n"
-            "Literal skill form: /speckit-plan\n"
+            "Literal slash form: /speckit.foo.bar --flag value\n"
+            "Native slash form: /speckit-foo-bar\n"
+            "Native dollar form: $speckit-foo-bar\n"
+            "Native skill form: /skill:speckit-foo-bar\n"
             "Literal bare form: speckit.foo.bar\n"
+            "Path-like form: https://example.com/speckit.foo.bar\n"
+            "File-like form: /speckit.foo.bar.md\n"
         )
 
         manager = ExtensionManager(project_dir)
         manager.install_from_directory(ext_dir, "0.1.0", register_commands=False)
 
         content = (skills_dir / "speckit-literal-ref-ext-run" / "SKILL.md").read_text()
-        assert "/speckit.foo.bar" in content
-        assert "/speckit-plan" in content
+        assert f"Literal slash form: {expected_invocation} --flag value" in content
+        assert "Literal slash form: /speckit.foo.bar --flag value" not in content
+        assert "Native slash form: /speckit-foo-bar" in content
+        assert "Native dollar form: $speckit-foo-bar" in content
+        assert "Native skill form: /skill:speckit-foo-bar" in content
         assert "speckit.foo.bar" in content
-        assert "/speckit-foo-bar" not in content
-        assert "$speckit-plan" not in content
+        assert "https://example.com/speckit.foo.bar" in content
+        assert "/speckit.foo.bar.md" in content
 
     def test_missing_command_file_skipped(self, skills_project, temp_dir):
         """Commands with missing source files should be skipped gracefully."""