fix extension-local script path rewriting

src/specify_cli/agents.py

@@ -148,7 +148,9 @@ def render_frontmatter(fm: dict) -> str:
         )
         return f"---\n{yaml_str}---\n"
 
-    def _adjust_script_paths(self, frontmatter: dict) -> dict:
+    def _adjust_script_paths(
+        self, frontmatter: dict, extension_id: Optional[str] = None
+    ) -> dict:
         """Normalize script paths in frontmatter to generated project locations.
 
         Rewrites known repo-relative and top-level script paths under the
@@ -158,6 +160,7 @@ def _adjust_script_paths(self, frontmatter: dict) -> dict:
 
         Args:
             frontmatter: Frontmatter dictionary
+            extension_id: Extension id when rendering extension-owned commands.
 
         Returns:
             Modified frontmatter with normalized project paths
@@ -168,11 +171,15 @@ def _adjust_script_paths(self, frontmatter: dict) -> dict:
         if isinstance(scripts, dict):
             for key, script_path in scripts.items():
                 if isinstance(script_path, str):
-                    scripts[key] = self.rewrite_project_relative_paths(script_path)
+                    scripts[key] = self.rewrite_project_relative_paths(
+                        script_path, extension_id=extension_id
+                    )
         return frontmatter
 
     @staticmethod
-    def rewrite_project_relative_paths(text: str) -> str:
+    def rewrite_project_relative_paths(
+        text: str, extension_id: Optional[str] = None
+    ) -> str:
         """Rewrite repo-relative paths to their generated project locations."""
         if not isinstance(text, str) or not text:
             return text
@@ -184,10 +191,18 @@ def rewrite_project_relative_paths(text: str) -> str:
         ):
             text = text.replace(old, new)
 
-        # Only rewrite top-level style references so extension-local paths like
-        # ".specify/extensions/<ext>/scripts/..." remain intact.
+        # Only rewrite top-level style references so existing generated paths
+        # like ".specify/extensions/<ext>/scripts/..." remain intact. When
+        # rendering extension commands, top-level "scripts/" is extension-local.
+        scripts_replacement = (
+            f".specify/extensions/{extension_id}/scripts/"
+            if extension_id
+            else ".specify/scripts/"
+        )
         text = re.sub(r'(^|[\s`"\'(])(?:\.?/)?memory/', r"\1.specify/memory/", text)
-        text = re.sub(r'(^|[\s`"\'(])(?:\.?/)?scripts/', r"\1.specify/scripts/", text)
+        text = re.sub(
+            r'(^|[\s`"\'(])(?:\.?/)?scripts/', rf"\1{scripts_replacement}", text
+        )
         text = re.sub(
             r'(^|[\s`"\'(])(?:\.?/)?templates/', r"\1.specify/templates/", text
         )
@@ -312,6 +327,7 @@ def render_skill_command(
         source_id: str,
         source_file: str,
         project_root: Path,
+        extension_id: Optional[str] = None,
     ) -> str:
         """Render a command override as a SKILL.md file.
 
@@ -331,7 +347,7 @@ def render_skill_command(
         agent_config = self.AGENT_CONFIGS.get(agent_name, {})
         if agent_config.get("extension") == "/SKILL.md":
             body = self.resolve_skill_placeholders(
-                agent_name, frontmatter, body, project_root
+                agent_name, frontmatter, body, project_root, extension_id=extension_id
             )
 
         description = frontmatter.get(
@@ -393,7 +409,11 @@ def apply_argument_hint(
 
     @staticmethod
     def resolve_skill_placeholders(
-        agent_name: str, frontmatter: dict, body: str, project_root: Path
+        agent_name: str,
+        frontmatter: dict,
+        body: str,
+        project_root: Path,
+        extension_id: Optional[str] = None,
     ) -> str:
         """Resolve script placeholders for skills-backed agents."""
         if not isinstance(frontmatter, dict):
@@ -433,7 +453,9 @@ def resolve_skill_placeholders(
 
         body = body.replace("{ARGS}", "$ARGUMENTS").replace("__AGENT__", agent_name)
 
-        return CommandRegistrar.rewrite_project_relative_paths(body)
+        return CommandRegistrar.rewrite_project_relative_paths(
+            body, extension_id=extension_id
+        )
 
     def _convert_argument_placeholder(
         self, content: str, from_placeholder: str, to_placeholder: str
@@ -528,6 +550,7 @@ def register_commands(
         context_note: str = None,
         _resolved_dir: Path = None,
         link_outputs: bool = False,
+        extension_id: Optional[str] = None,
     ) -> List[str]:
         """Register commands for a specific agent.
 
@@ -545,6 +568,7 @@ def register_commands(
             link_outputs: If True, write rendered output to a source-local
                 dev cache and symlink the agent command file to it. Falls back
                 to a normal file write when symlinks are unavailable.
+            extension_id: Extension id when rendering extension-owned commands.
 
         Returns:
             List of registered command names
@@ -614,7 +638,9 @@ def register_commands(
                         frontmatter[key] = core_frontmatter[key]
                 frontmatter.pop("strategy", None)
 
-            frontmatter = self._adjust_script_paths(frontmatter)
+            frontmatter = self._adjust_script_paths(
+                frontmatter, extension_id=extension_id
+            )
 
             for key in agent_config.get("strip_frontmatter_keys", []):
                 frontmatter.pop(key, None)
@@ -653,10 +679,11 @@ def register_commands(
                     source_id,
                     cmd_file,
                     project_root,
+                    extension_id=extension_id,
                 )
             elif agent_config["format"] == "markdown":
                 body = self.resolve_skill_placeholders(
-                    agent_name, frontmatter, body, project_root
+                    agent_name, frontmatter, body, project_root, extension_id=extension_id
                 )
                 body = self._convert_argument_placeholder(
                     body, "$ARGUMENTS", agent_config["args"]
@@ -666,7 +693,7 @@ def register_commands(
                 )
             elif agent_config["format"] == "toml":
                 body = self.resolve_skill_placeholders(
-                    agent_name, frontmatter, body, project_root
+                    agent_name, frontmatter, body, project_root, extension_id=extension_id
                 )
                 body = self._convert_argument_placeholder(
                     body, "$ARGUMENTS", agent_config["args"]
@@ -721,6 +748,7 @@ def register_commands(
                             source_id,
                             cmd_file,
                             project_root,
+                            extension_id=extension_id,
                         )
                     elif agent_config["format"] == "markdown":
                         alias_output = self.render_markdown_command(
@@ -750,6 +778,7 @@ def register_commands(
                             source_id,
                             cmd_file,
                             project_root,
+                            extension_id=extension_id,
                         )
 
                 alias_file = (
@@ -881,6 +910,7 @@ def register_commands_for_all_agents(
         context_note: str = None,
         link_outputs: bool = False,
         create_missing_active_skills_dir: bool = False,
+        extension_id: Optional[str] = None,
     ) -> Dict[str, List[str]]:
         """Register commands for all detected agents in the project.
 
@@ -897,6 +927,7 @@ def register_commands_for_all_agents(
                 Recovery requires active skills mode (or Kimi's existing native
                 skills directory) and is skipped when safe resolution or
                 creation fails.
+            extension_id: Extension id when rendering extension-owned commands.
 
         Returns:
             Dictionary mapping agent names to list of registered commands
@@ -999,6 +1030,7 @@ def register_commands_for_all_agents(
                         context_note=context_note,
                         _resolved_dir=agent_dir,
                         link_outputs=link_outputs,
+                        extension_id=extension_id,
                     )
                     if registered:
                         results[agent_name] = registered
@@ -1023,6 +1055,7 @@ def register_commands_for_non_skill_agents(
         project_root: Path,
         context_note: Optional[str] = None,
         link_outputs: bool = False,
+        extension_id: Optional[str] = None,
     ) -> Dict[str, List[str]]:
         """Register commands for all non-skill agents in the project.
 
@@ -1038,6 +1071,7 @@ def register_commands_for_non_skill_agents(
             context_note: Custom context comment for markdown output
             link_outputs: If True, create dev-mode symlinks for rendered
                 command files when supported by the OS.
+            extension_id: Extension id when rendering extension-owned commands.
 
         Returns:
             Dictionary mapping agent names to list of registered commands
@@ -1066,6 +1100,7 @@ def register_commands_for_non_skill_agents(
                         context_note=context_note,
                         _resolved_dir=agent_dir,
                         link_outputs=link_outputs,
+                        extension_id=extension_id,
                     )
                     if registered:
                         results[agent_name] = registered

src/specify_cli/extensions/__init__.py

@@ -1075,9 +1075,11 @@ def _register_extension_skills(
                         pass  # best-effort cleanup
                 continue
             frontmatter, body = registrar.parse_frontmatter(content)
-            frontmatter = registrar._adjust_script_paths(frontmatter)
+            frontmatter = registrar._adjust_script_paths(
+                frontmatter, extension_id=manifest.id
+            )
             body = registrar.resolve_skill_placeholders(
-                selected_ai, frontmatter, body, self.project_root
+                selected_ai, frontmatter, body, self.project_root, extension_id=manifest.id
             )
 
             original_desc = frontmatter.get("description", "")
@@ -1958,6 +1960,7 @@ def register_commands_for_agent(
             project_root,
             context_note=context_note,
             link_outputs=link_outputs,
+            extension_id=manifest.id,
         )
 
     def register_commands_for_all_agents(
@@ -1978,6 +1981,7 @@ def register_commands_for_all_agents(
             context_note=context_note,
             link_outputs=link_outputs,
             create_missing_active_skills_dir=create_missing_active_skills_dir,
+            extension_id=manifest.id,
         )
 
     def unregister_commands(

tests/test_extension_skills.py

@@ -850,6 +850,67 @@ def test_skill_registration_resolves_script_placeholders(self, project_dir, temp
         assert ".specify/templates/checklist.md" in content
         assert ".specify/memory/constitution.md" in content
 
+    def test_skill_registration_uses_extension_local_script_paths(self, project_dir, temp_dir):
+        """Auto-registered skills should not rewrite extension scripts into core scripts."""
+        _create_init_options(project_dir, ai="claude", ai_skills=True)
+        skills_dir = _create_skills_dir(project_dir, ai="claude")
+
+        ext_dir = temp_dir / "scripted-ext"
+        ext_dir.mkdir()
+        manifest_data = {
+            "schema_version": "1.0",
+            "extension": {
+                "id": "scripted-ext",
+                "name": "Scripted Extension",
+                "version": "1.0.0",
+                "description": "Test",
+            },
+            "requires": {"speckit_version": ">=0.1.0"},
+            "provides": {
+                "commands": [
+                    {
+                        "name": "speckit.scripted-ext.check",
+                        "file": "commands/check.md",
+                        "description": "Scripted check command",
+                    }
+                ]
+            },
+        }
+        with open(ext_dir / "extension.yml", "w") as f:
+            yaml.safe_dump(manifest_data, f)
+
+        (ext_dir / "commands").mkdir()
+        (ext_dir / "scripts" / "bash").mkdir(parents=True)
+        (ext_dir / "scripts" / "bash" / "resolve-skill.sh").write_text(
+            "#!/usr/bin/env bash\n"
+        )
+        (ext_dir / "scripts" / "bash" / "ensure-skills.sh").write_text(
+            "#!/usr/bin/env bash\n"
+        )
+        (ext_dir / "commands" / "check.md").write_text(
+            "---\n"
+            "description: Scripted check command\n"
+            "scripts:\n"
+            '  sh: scripts/bash/resolve-skill.sh "{ARGS}"\n'
+            "---\n\n"
+            "Run {SCRIPT}\n"
+            "Then run scripts/bash/ensure-skills.sh.\n"
+        )
+
+        manager = ExtensionManager(project_dir)
+        manager.install_from_directory(ext_dir, "0.1.0", register_commands=False)
+
+        content = (skills_dir / "speckit-scripted-ext-check" / "SKILL.md").read_text()
+        assert "{SCRIPT}" not in content
+        assert "{ARGS}" not in content
+        assert (
+            '.specify/extensions/scripted-ext/scripts/bash/resolve-skill.sh "$ARGUMENTS"'
+            in content
+        )
+        assert ".specify/extensions/scripted-ext/scripts/bash/ensure-skills.sh" in content
+        assert ".specify/scripts/bash/resolve-skill.sh" not in content
+        assert ".specify/scripts/bash/ensure-skills.sh" not in content
+
     def test_missing_command_file_skipped(self, skills_project, temp_dir):
         """Commands with missing source files should be skipped gracefully."""
         project_dir, skills_dir = skills_project

tests/test_extensions.py

@@ -1146,10 +1146,12 @@ def fake_register_all(
             context_note=None,
             link_outputs=False,
             create_missing_active_skills_dir=False,
+            extension_id=None,
         ):
             captured["create_missing_active_skills_dir"] = (
                 create_missing_active_skills_dir
             )
+            captured["extension_id"] = extension_id
             return {}
 
         monkeypatch.setattr(
@@ -1163,6 +1165,7 @@ def fake_register_all(
         registrar.register_commands_for_all_agents(manifest, extension_dir, project_dir)
 
         assert captured["create_missing_active_skills_dir"] is False
+        assert captured["extension_id"] == manifest.id
 
     def test_install_duplicate(self, extension_dir, project_dir):
         """Test installing already installed extension."""
@@ -1694,6 +1697,29 @@ def test_adjust_script_paths_preserves_extension_local_paths(self):
         assert adjusted["scripts"]["sh"] == ".specify/extensions/test-ext/scripts/setup.sh {ARGS}"
         assert adjusted["scripts"]["ps"] == ".specify/scripts/powershell/setup-plan.ps1 {ARGS}"
 
+    def test_adjust_script_paths_rewrites_extension_top_level_scripts(self):
+        """Extension command-local scripts should resolve under the installed extension."""
+        from specify_cli.agents import CommandRegistrar as AgentCommandRegistrar
+
+        registrar = AgentCommandRegistrar()
+        original = {
+            "scripts": {
+                "sh": "scripts/bash/resolve-skill.sh {ARGS}",
+                "ps": "../../scripts/powershell/setup-plan.ps1 -Json",
+            }
+        }
+
+        adjusted = registrar._adjust_script_paths(original, extension_id="test-ext")
+
+        assert (
+            adjusted["scripts"]["sh"]
+            == ".specify/extensions/test-ext/scripts/bash/resolve-skill.sh {ARGS}"
+        )
+        assert (
+            adjusted["scripts"]["ps"]
+            == ".specify/scripts/powershell/setup-plan.ps1 -Json"
+        )
+
     def test_rewrite_project_relative_paths_preserves_extension_local_body_paths(self):
         """Body rewrites should preserve extension-local assets while fixing top-level refs."""
         from specify_cli.agents import CommandRegistrar as AgentCommandRegistrar
@@ -1708,6 +1734,24 @@ def test_rewrite_project_relative_paths_preserves_extension_local_body_paths(sel
         assert ".specify/extensions/test-ext/templates/spec.md" in rewritten
         assert ".specify/scripts/bash/setup-plan.sh" in rewritten
 
+    def test_rewrite_project_relative_paths_uses_extension_context_for_scripts(self):
+        """Extension source bodies treat top-level scripts/ as extension-local."""
+        from specify_cli.agents import CommandRegistrar as AgentCommandRegistrar
+
+        body = (
+            "Run scripts/bash/ensure-skills.sh\n"
+            "Fallback ../../scripts/bash/setup-plan.sh\n"
+            "Read templates/checklist.md\n"
+        )
+
+        rewritten = AgentCommandRegistrar.rewrite_project_relative_paths(
+            body, extension_id="test-ext"
+        )
+
+        assert ".specify/extensions/test-ext/scripts/bash/ensure-skills.sh" in rewritten
+        assert ".specify/scripts/bash/setup-plan.sh" in rewritten
+        assert ".specify/templates/checklist.md" in rewritten
+
     def test_render_toml_command_handles_embedded_triple_double_quotes(self):
         """TOML renderer should stay valid when body includes triple double-quotes."""
         from specify_cli.agents import CommandRegistrar as AgentCommandRegistrar