specfact-cli 0.46.18__tar.gz → 0.46.25__tar.gz

{specfact_cli-0.46.18 → specfact_cli-0.46.25}/.gitignore

@@ -113,6 +113,7 @@ docs/internal/
 .claude/commands/specfact.*.md
 .claude/skills/openspec-*/
 !.claude/skills/openspec-workflows/
+.claude/settings.json
 
 .codex/skills/openspec-*/
 !.codex/skills/openspec-workflows/

{specfact_cli-0.46.18 → specfact_cli-0.46.25}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: specfact-cli
-Version: 0.46.18
+Version: 0.46.25
 Summary: The swiss knife CLI for agile DevOps teams. Keep backlog, specs, tests, and code in sync with validation and contract enforcement for new projects and long-lived codebases.
 Project-URL: Homepage, https://github.com/nold-ai/specfact-cli
 Project-URL: Repository, https://github.com/nold-ai/specfact-cli.git
@@ -224,6 +224,7 @@ Classifier: Topic :: Software Development :: Testing
 Requires-Python: >=3.11
 Requires-Dist: azure-identity>=1.17.1
 Requires-Dist: beartype>=0.22.4
+Requires-Dist: click<8.2,>=8.1.8
 Requires-Dist: commentjson>=0.9.0
 Requires-Dist: cryptography>=43.0.0
 Requires-Dist: gitpython>=3.1.45
@@ -232,14 +233,12 @@ Requires-Dist: icontract>=2.7.1
 Requires-Dist: jinja2>=3.1.6
 Requires-Dist: jsonschema>=4.23.0
 Requires-Dist: networkx>=3.4.2
-Requires-Dist: opentelemetry-exporter-otlp-proto-http>=1.27.0
-Requires-Dist: opentelemetry-sdk>=1.27.0
 Requires-Dist: packaging>=24.0
 Requires-Dist: pydantic>=2.12.3
 Requires-Dist: pyyaml>=6.0.3
 Requires-Dist: questionary>=2.0.1
 Requires-Dist: requests>=2.32.3
-Requires-Dist: rich<13.6.0,>=13.5.2
+Requires-Dist: rich<16.0.0,>=13.5.2
 Requires-Dist: ruamel-yaml>=0.18.16
 Requires-Dist: typer<0.24,>=0.20.0
 Requires-Dist: typing-extensions>=4.15.0
@@ -277,6 +276,9 @@ Requires-Dist: graphviz>=0.20.1; extra == 'enhanced-analysis'
 Requires-Dist: pycg==0.0.7; extra == 'enhanced-analysis'
 Provides-Extra: scanning
 Requires-Dist: semgrep>=1.144.0; extra == 'scanning'
+Provides-Extra: telemetry
+Requires-Dist: opentelemetry-exporter-otlp-proto-http>=1.27.0; extra == 'telemetry'
+Requires-Dist: opentelemetry-sdk>=1.27.0; extra == 'telemetry'
 Description-Content-Type: text/markdown
 
 # SpecFact CLI

{specfact_cli-0.46.18 → specfact_cli-0.46.25}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "specfact-cli"
-version = "0.46.18"
+version = "0.46.25"
 description = "The swiss knife CLI for agile DevOps teams. Keep backlog, specs, tests, and code in sync with validation and contract enforcement for new projects and long-lived codebases."
 readme = "README.md"
 requires-python = ">=3.11"
@@ -65,8 +65,9 @@ dependencies = [
 
     # CLI framework
     # Typer 0.24+ requires click>=8.2.1 (generic Choice[...]); dev semgrep pins click~=8.1.8 — cap Typer.
+    "click>=8.1.8,<8.2",
     "typer>=0.20.0,<0.24",
-    "rich>=13.5.2,<13.6.0",  # Compatible with semgrep (requires rich~=13.5.2)
+    "rich>=13.5.2,<16.0.0",  # Semgrep allows rich>=13.5.2; keep below next major.
     "questionary>=2.0.1",  # Interactive prompts with arrow key navigation
     
     # Template engine
@@ -94,10 +95,6 @@ dependencies = [
 
     # File system watching
     "watchdog>=6.0.0",
-
-    # Telemetry (opt-in; only active when SPECFACT_TELEMETRY_OPT_IN=true)
-    "opentelemetry-sdk>=1.27.0",
-    "opentelemetry-exporter-otlp-proto-http>=1.27.0",
 ]
 
 [project.optional-dependencies]
@@ -106,6 +103,11 @@ contracts = [
     "hypothesis>=6.142.4",
 ]
 
+telemetry = [
+    "opentelemetry-sdk>=1.27.0",
+    "opentelemetry-exporter-otlp-proto-http>=1.27.0",
+]
+
 dev = [
     "setuptools>=69.0.0,<82",
     "pytest>=8.4.2",
@@ -283,6 +285,7 @@ verify-removal-gate = [
     "hatch run verify-modules-signature",
 ]
 export-change-github = "python scripts/export-change-to-github.py {args}"
+runtime-discovery-smoke = "python scripts/runtime_discovery_smoke.py {args}"
 
 # Contract-First Smart Test System Scripts
 contract-test = "python tools/contract_first_smart_test.py run --level auto {args}"

{specfact_cli-0.46.18 → specfact_cli-0.46.25}/src/__init__.py

@@ -3,4 +3,4 @@ SpecFact CLI - Spec→Contract→Sentinel tool for contract-driven development.
 """
 
 # Package version: keep in sync with pyproject.toml, setup.py, src/specfact_cli/__init__.py
-__version__ = "0.46.18"
+__version__ = "0.46.25"

{specfact_cli-0.46.18 → specfact_cli-0.46.25}/src/specfact_cli/__init__.py

@@ -45,6 +45,6 @@ def _bootstrap_bundle_paths() -> None:
 
 _bootstrap_bundle_paths()
 
-__version__ = "0.46.18"
+__version__ = "0.46.25"
 
 __all__ = ["__version__"]

{specfact_cli-0.46.18 → specfact_cli-0.46.25}/src/specfact_cli/adapters/ado.py

@@ -1625,7 +1625,7 @@ class AdoAdapter(BridgeAdapter, BacklogAdapterMixin, BacklogAdapter):
         headers = {"Content-Type": "application/json-patch+json", **self._auth_headers()}
         try:
             response = self._request_with_retry(
-                lambda: requests.patch(url, json=patch_document, headers=headers, timeout=30)
+                lambda: requests.patch(url, json=cast(Any, patch_document), headers=headers, timeout=30)
             )
         except requests.RequestException as exc:
             resp = getattr(exc, "response", None)
@@ -1939,7 +1939,7 @@ class AdoAdapter(BridgeAdapter, BacklogAdapterMixin, BacklogAdapter):
             # Refresh failed (no cached refresh token, refresh token expired, etc.)
             return None
 
-    def _auth_headers(self) -> dict[str, str]:
+    def _auth_headers(self) -> dict[str, str | bytes]:
         """Return authorization headers based on token type."""
         if not self.api_token:
             return {}
@@ -1953,7 +1953,7 @@ class AdoAdapter(BridgeAdapter, BacklogAdapterMixin, BacklogAdapter):
         self,
         url: str,
         *,
-        headers: dict[str, str] | None = None,
+        headers: dict[str, str | bytes] | None = None,
         params: dict[str, Any] | None = None,
         timeout: int = 30,
         retry_on_ambiguous_transport: bool = True,
@@ -1973,7 +1973,7 @@ class AdoAdapter(BridgeAdapter, BacklogAdapterMixin, BacklogAdapter):
         self,
         url: str,
         *,
-        headers: dict[str, str] | None = None,
+        headers: dict[str, str | bytes] | None = None,
         params: dict[str, Any] | None = None,
         json: dict[str, Any] | None = None,
         timeout: int = 30,
@@ -2213,7 +2213,7 @@ class AdoAdapter(BridgeAdapter, BacklogAdapterMixin, BacklogAdapter):
 
         try:
             response = self._request_with_retry(
-                lambda: requests.post(url, json=patch_document, headers=headers, timeout=30),
+                lambda: requests.post(url, json=cast(Any, patch_document), headers=headers, timeout=30),
                 retry_on_ambiguous_transport=False,
             )
             if is_debug_mode():
@@ -2670,7 +2670,7 @@ class AdoAdapter(BridgeAdapter, BacklogAdapterMixin, BacklogAdapter):
 
         try:
             response = self._request_with_retry(
-                lambda: requests.post(url, json=comment_body, headers=headers, timeout=30),
+                lambda: requests.post(url, json=cast(Any, comment_body), headers=headers, timeout=30),
                 retry_on_ambiguous_transport=False,
             )
             comment_data = response.json()
@@ -3478,7 +3478,7 @@ class AdoAdapter(BridgeAdapter, BacklogAdapterMixin, BacklogAdapter):
             **self._auth_headers(),
         }
         response = self._request_with_retry(
-            lambda: requests.post(url, json=patch_document, headers=headers, timeout=30),
+            lambda: requests.post(url, json=cast(Any, patch_document), headers=headers, timeout=30),
             retry_on_ambiguous_transport=False,
         )
         created = response.json()
@@ -3782,7 +3782,7 @@ class AdoAdapter(BridgeAdapter, BacklogAdapterMixin, BacklogAdapter):
         if operations_no_format == operations:
             return None
         try:
-            resp = requests.patch(url, headers=headers, json=operations_no_format, timeout=30)
+            resp = requests.patch(url, headers=headers, json=cast(Any, operations_no_format), timeout=30)
             resp.raise_for_status()
             return resp
         except requests.HTTPError as retry_error:
@@ -3802,7 +3802,7 @@ class AdoAdapter(BridgeAdapter, BacklogAdapterMixin, BacklogAdapter):
     ) -> requests.Response | None:
         operations_replace = self._backlog_ops_replace_multiline_add_with_replace(operations)
         try:
-            resp = requests.patch(url, headers=headers, json=operations_replace, timeout=30)
+            resp = requests.patch(url, headers=headers, json=cast(Any, operations_replace), timeout=30)
             resp.raise_for_status()
             return resp
         except requests.HTTPError:
@@ -3820,7 +3820,7 @@ class AdoAdapter(BridgeAdapter, BacklogAdapterMixin, BacklogAdapter):
         )
         operations_html = self._backlog_ops_convert_markdown_fields_to_html(operations)
         try:
-            resp = requests.patch(url, headers=headers, json=operations_html, timeout=30)
+            resp = requests.patch(url, headers=headers, json=cast(Any, operations_html), timeout=30)
             resp.raise_for_status()
             return resp
         except requests.HTTPError:
@@ -3834,7 +3834,9 @@ class AdoAdapter(BridgeAdapter, BacklogAdapterMixin, BacklogAdapter):
         operations: list[dict[str, Any]],
     ) -> requests.Response:
         try:
-            return self._request_with_retry(lambda: requests.patch(url, headers=headers, json=operations, timeout=30))
+            return self._request_with_retry(
+                lambda: requests.patch(url, headers=headers, json=cast(Any, operations), timeout=30)
+            )
         except requests.HTTPError as e:
             user_msg = _log_ado_patch_failure(e.response, operations, url)
             e.ado_user_message = user_msg  # type: ignore[attr-defined]

{specfact_cli-0.46.18 → specfact_cli-0.46.25}/src/specfact_cli/adapters/github.py

@@ -561,7 +561,7 @@ class GitHubAdapter(BridgeAdapter, BacklogAdapterMixin, BacklogAdapter):
         from specfact_cli.backlog.converter import convert_github_issue_to_backlog_item
 
         url = f"{self.base_url}/search/issues"
-        headers = {
+        headers: dict[str, str | bytes] = {
             "Authorization": f"token {self.api_token}",
             "Accept": "application/vnd.github.v3+json",
         }
@@ -1232,7 +1232,7 @@ class GitHubAdapter(BridgeAdapter, BacklogAdapterMixin, BacklogAdapter):
 
         repo_owner, repo_name, issue_number = self._parse_issue_reference(item_ref)
         url = f"{self.base_url}/repos/{repo_owner}/{repo_name}/issues/{issue_number}"
-        headers = {
+        headers: dict[str, str | bytes] = {
             "Authorization": f"token {self.api_token}",
             "Accept": "application/vnd.github.v3+json",
         }
@@ -1498,7 +1498,7 @@ class GitHubAdapter(BridgeAdapter, BacklogAdapterMixin, BacklogAdapter):
 
         # Create issue via GitHub API
         url = f"{self.base_url}/repos/{repo_owner}/{repo_name}/issues"
-        headers = {
+        headers: dict[str, str | bytes] = {
             "Authorization": f"token {self.api_token}",
             "Accept": "application/vnd.github.v3+json",
         }
@@ -1592,7 +1592,7 @@ class GitHubAdapter(BridgeAdapter, BacklogAdapterMixin, BacklogAdapter):
 
         # Update issue state
         url = f"{self.base_url}/repos/{repo_owner}/{repo_name}/issues/{issue_number}"
-        headers = {
+        headers: dict[str, str | bytes] = {
             "Authorization": f"token {self.api_token}",
             "Accept": "application/vnd.github.v3+json",
         }
@@ -1601,7 +1601,9 @@ class GitHubAdapter(BridgeAdapter, BacklogAdapterMixin, BacklogAdapter):
             payload["state_reason"] = state_reason
 
         try:
-            response = self._request_with_retry(lambda: requests.patch(url, json=payload, headers=headers, timeout=30))
+            response = self._request_with_retry(
+                lambda: requests.patch(url, json=cast(Any, payload), headers=headers, timeout=30)
+            )
             issue_data = response.json()
 
             # Add comment explaining status change
@@ -1634,7 +1636,7 @@ class GitHubAdapter(BridgeAdapter, BacklogAdapterMixin, BacklogAdapter):
             return []
 
         url = f"{self.base_url}/repos/{repo_owner}/{repo_name}/issues/{issue_number}/comments"
-        headers = {
+        headers: dict[str, str | bytes] = {
             "Authorization": f"token {self.api_token}",
             "Accept": "application/vnd.github.v3+json",
         }
@@ -1658,7 +1660,7 @@ class GitHubAdapter(BridgeAdapter, BacklogAdapterMixin, BacklogAdapter):
             comment: Comment text
         """
         url = f"{self.base_url}/repos/{repo_owner}/{repo_name}/issues/{issue_number}/comments"
-        headers = {
+        headers: dict[str, str | bytes] = {
             "Authorization": f"token {self.api_token}",
             "Accept": "application/vnd.github.v3+json",
         }
@@ -1666,7 +1668,7 @@ class GitHubAdapter(BridgeAdapter, BacklogAdapterMixin, BacklogAdapter):
 
         try:
             self._request_with_retry(
-                lambda: requests.post(url, json=payload, headers=headers, timeout=30),
+                lambda: requests.post(url, json=cast(Any, payload), headers=headers, timeout=30),
                 retry_on_ambiguous_transport=False,
             )
         except requests.RequestException as e:
@@ -1676,7 +1678,7 @@ class GitHubAdapter(BridgeAdapter, BacklogAdapterMixin, BacklogAdapter):
     def _fetch_issue_snapshot(self, repo_owner: str, repo_name: str, issue_number: int) -> tuple[str, str, str]:
         """Fetch current issue body, title, and state for preservation-aware updates."""
         url = f"{self.base_url}/repos/{repo_owner}/{repo_name}/issues/{issue_number}"
-        headers = {
+        headers: dict[str, str | bytes] = {
             "Authorization": f"token {self.api_token}",
             "Accept": "application/vnd.github.v3+json",
         }
@@ -1759,7 +1761,7 @@ class GitHubAdapter(BridgeAdapter, BacklogAdapterMixin, BacklogAdapter):
 
         # Update issue body via GitHub API PATCH
         url = f"{self.base_url}/repos/{repo_owner}/{repo_name}/issues/{issue_number}"
-        headers = {
+        headers: dict[str, str | bytes] = {
             "Authorization": f"token {self.api_token}",
             "Accept": "application/vnd.github.v3+json",
         }
@@ -1969,7 +1971,7 @@ class GitHubAdapter(BridgeAdapter, BacklogAdapterMixin, BacklogAdapter):
 
         # Get current issue to retrieve existing labels
         url = f"{self.base_url}/repos/{repo_owner}/{repo_name}/issues/{issue_number}"
-        headers = {
+        headers: dict[str, str | bytes] = {
             "Authorization": f"token {self.api_token}",
             "Accept": "application/vnd.github.v3+json",
         }
@@ -1987,7 +1989,9 @@ class GitHubAdapter(BridgeAdapter, BacklogAdapterMixin, BacklogAdapter):
             patch_url = f"{self.base_url}/repos/{repo_owner}/{repo_name}/issues/{issue_number}"
             patch_payload = {"labels": all_labels}
 
-            self._request_with_retry(lambda: requests.patch(patch_url, json=patch_payload, headers=headers, timeout=30))
+            self._request_with_retry(
+                lambda: requests.patch(patch_url, json=cast(Any, patch_payload), headers=headers, timeout=30)
+            )
 
             return {
                 "issue_number": current_issue.get("number", issue_number),  # Use API response number (int)
@@ -2623,7 +2627,7 @@ class GitHubAdapter(BridgeAdapter, BacklogAdapterMixin, BacklogAdapter):
             return None
 
         url = f"{self.base_url}/repos/{self.repo_owner}/{self.repo_name}/issues/{normalized_id}"
-        headers = {
+        headers: dict[str, str | bytes] = {
             "Authorization": f"token {self.api_token}",
             "Accept": "application/vnd.github.v3+json",
         }
@@ -2761,7 +2765,7 @@ class GitHubAdapter(BridgeAdapter, BacklogAdapterMixin, BacklogAdapter):
     @beartype
     def _github_graphql(self, query: str, variables: dict[str, Any]) -> dict[str, Any]:
         """Execute GitHub GraphQL request and return `data` payload."""
-        headers = {
+        headers: dict[str, str | bytes] = {
             "Authorization": f"token {self.api_token}",
             "Accept": "application/vnd.github+json",
         }
@@ -2976,14 +2980,14 @@ class GitHubAdapter(BridgeAdapter, BacklogAdapterMixin, BacklogAdapter):
             issue_type, str(payload.get("priority") or "").strip(), payload.get("story_points")
         )
         url = f"{self.base_url}/repos/{owner}/{repo}/issues"
-        headers = {
+        headers: dict[str, str | bytes] = {
             "Authorization": f"token {self.api_token}",
             "Accept": "application/vnd.github.v3+json",
         }
         response = self._request_with_retry(
             lambda: requests.post(
                 url,
-                json={"title": title, "body": body, "labels": labels},
+                json=cast(Any, {"title": title, "body": body, "labels": labels}),
                 headers=headers,
                 timeout=30,
             ),
@@ -3245,7 +3249,7 @@ class GitHubAdapter(BridgeAdapter, BacklogAdapterMixin, BacklogAdapter):
 
         issue_number = int(item.id)
         url = f"{self.base_url}/repos/{self.repo_owner}/{self.repo_name}/issues/{issue_number}"
-        headers = {
+        headers: dict[str, str | bytes] = {
             "Authorization": f"token {self.api_token}",
             "Accept": "application/vnd.github.v3+json",
         }

{specfact_cli-0.46.18 → specfact_cli-0.46.25}/src/specfact_cli/cli.py

@@ -178,6 +178,11 @@ class _RootCLIGroup(ProgressiveDisclosureGroup):
                 _print_missing_bundle_command_help(invoked)
                 raise SystemExit(1) from None
             raise
+        except ValueError as exc:
+            if invoked in KNOWN_BUNDLE_GROUP_OR_SHIM_NAMES:
+                _print_missing_bundle_command_help(invoked)
+                raise SystemExit(1) from exc
+            raise
         _name, cmd, remaining = result
         if cmd is not None or not remaining:
             return result
@@ -693,6 +698,8 @@ class _LazyDelegateGroup(click.Group):
         real_group = self._get_real_click_group()
         if real_group is not None:
             return real_group.get_command(ctx, cmd_name)
+        if self._lazy_cmd_name in KNOWN_BUNDLE_GROUP_OR_SHIM_NAMES:
+            return self._delegate_cmd
         return None
 
     def _get_real_click_group(self) -> click.Group | None:

{specfact_cli-0.46.18 → specfact_cli-0.46.25}/src/specfact_cli/models/project.py

@@ -662,7 +662,13 @@ class ProjectBundle(BaseModel):
         if progress_callback:
             progress_callback(total_artifacts, total_artifacts, "bundle.manifest.yaml")
         manifest_path = bundle_dir / "bundle.manifest.yaml"
-        dump_structured_file(self.manifest.model_dump(mode="json"), manifest_path)
+        manifest_data = self.manifest.model_dump(mode="json")
+        if num_features > 1000:
+            import json
+
+            manifest_path.write_text(json.dumps(manifest_data, indent=2), encoding="utf-8")
+        else:
+            dump_structured_file(manifest_data, manifest_path)
 
     @beartype
     @require(lambda self, key: isinstance(key, str) and len(key) > 0, "Feature key must be non-empty string")

{specfact_cli-0.46.18 → specfact_cli-0.46.25}/src/specfact_cli/modules/init/module-package.yaml

@@ -1,5 +1,5 @@
 name: init
-version: 0.1.31
+version: 0.1.33
 commands:
   - init
 category: core
@@ -17,5 +17,5 @@ publisher:
 description: Initialize SpecFact workspace and bootstrap local configuration.
 license: Apache-2.0
 integrity:
-  checksum: sha256:0f7bc54a823bea14033fcb143ecb6c83d2bca2b5da661f03a0b545100acebe5b
-  signature: dTatkqgBUtti4tL/pmcFBZY9bsJ61gY/V0lP9gZU8Y5W3YWK+wpgRx1oewlAmfKzkxca2NhalKcjLACQjTNvAA==
+  checksum: sha256:0086a4fa3e1f8744deee21640e73e6e2f24daf2b4a680b9157feed5487afc208
+  signature: L7DtVqvg+zqc/CgJu/mOkvxYpfH9HuddbLS3EK5Uvnf6K/j/BofqopamZDdHVlevOGAb+dbsk06kskNOIJfkDQ==

{specfact_cli-0.46.18 → specfact_cli-0.46.25}/src/specfact_cli/modules/init/src/commands.py

@@ -26,7 +26,13 @@ from specfact_cli.registry.module_state import write_modules_state
 from specfact_cli.runtime import debug_print, is_non_interactive
 from specfact_cli.telemetry import telemetry
 from specfact_cli.utils.contract_predicates import repo_path_exists, repo_path_is_dir
-from specfact_cli.utils.env_manager import EnvManager, EnvManagerInfo, build_tool_command, detect_env_manager
+from specfact_cli.utils.env_manager import (
+    EnvManager,
+    EnvManagerInfo,
+    build_tool_command,
+    detect_env_manager,
+    env_info_from_tool_choice,
+)
 from specfact_cli.utils.ide_setup import (
     IDE_CONFIG,
     PROMPT_SOURCE_CORE,
@@ -610,6 +616,11 @@ def init_ide(
         "--ide",
         help="IDE type (cursor, vscode, copilot, claude, gemini, qwen, opencode, windsurf, kilocode, auggie, roo, codebuddy, amp, q, auto)",
     ),
+    env_manager: EnvManager = typer.Option(
+        EnvManager.AUTO,
+        "--env-manager",
+        help="Environment manager override: auto, uv, hatch, poetry, or pip",
+    ),
     prompts: str | None = typer.Option(
         None,
         "--prompts",
@@ -638,7 +649,17 @@ def init_ide(
     console.print(f"[cyan]IDE:[/cyan] {ide_name} ({selected_ide})")
     console.print()
 
-    env_info = detect_env_manager(repo_path)
+    env_info = (
+        detect_env_manager(repo_path)
+        if env_manager is EnvManager.AUTO
+        else env_info_from_tool_choice(env_manager, repo_path)
+    )
+    if env_manager is not EnvManager.AUTO and not env_info.available:
+        console.print(Panel(f"[bold red]{env_info.message}[/bold red]", border_style="red"))
+        raise typer.Exit(1)
+    if env_info.manager is not EnvManager.UNKNOWN:
+        console.print(f"[cyan]Environment manager:[/cyan] {env_info.manager.value}")
+        console.print()
     if env_info.manager == EnvManager.UNKNOWN:
         console.print(
             Panel(
@@ -673,7 +694,12 @@ def init_ide(
     copied_files, settings_path = copy_templates_to_ide(
         repo_path, selected_ide, force, prompts_by_source=selected_catalog
     )
-    write_ide_prompt_export_state(repo_path, selected_ide, sorted(selected_catalog.keys()))
+    write_ide_prompt_export_state(
+        repo_path,
+        selected_ide,
+        sorted(selected_catalog.keys()),
+        env_manager=env_info.manager.value,
+    )
     _copy_backlog_field_mapping_templates(repo_path, force, console)
 
     console.print()

{specfact_cli-0.46.18 → specfact_cli-0.46.25}/src/specfact_cli/modules/module_registry/module-package.yaml

@@ -1,5 +1,5 @@
 name: module-registry
-version: 0.1.23
+version: 0.1.26
 commands:
   - module
 category: core
@@ -17,5 +17,5 @@ publisher:
 description: 'Manage modules: search, list, show, install, and upgrade.'
 license: Apache-2.0
 integrity:
-  checksum: sha256:f500281d2249d712be23a1b25b5660374694dfa47634f60ae4378eb2cdb753ca
-  signature: cunuat95bD44IcNUBs35NTlHYOR8atydVz4ZyZTjIzwJL6Wz5YOfBYGq/WtgDnOFv3KplfvhRZbTo3CwmS/KBQ==
+  checksum: sha256:52a65869fb3d2d36910308c954e0ba199cb1c73f24136ee0d4aa7254f0996a22
+  signature: Uo2eJ40HiWBqe77N8gjiDg7zGhsvJE/hN82+Jcto7yUoqbH7bidLw9DfVQ0CrJfgM9Y0XHAUS1+LMyPr1jAaBg==

{specfact_cli-0.46.18 → specfact_cli-0.46.25}/src/specfact_cli/modules/module_registry/src/commands.py

@@ -5,6 +5,7 @@ from __future__ import annotations
 import inspect
 import os
 import shutil
+import tempfile
 from collections.abc import Callable, Iterator
 from contextlib import contextmanager
 from dataclasses import dataclass
@@ -27,7 +28,12 @@ from specfact_cli.registry.alias_manager import create_alias, list_aliases, remo
 from specfact_cli.registry.custom_registries import add_registry, fetch_all_indexes, list_registries, remove_registry
 from specfact_cli.registry.help_cache import run_discovery_and_write_cache
 from specfact_cli.registry.marketplace_client import fetch_registry_index
-from specfact_cli.registry.module_discovery import discover_all_modules, discover_all_modules_for_project
+from specfact_cli.registry.module_discovery import (
+    DiscoveredModule,
+    discover_all_modules,
+    discover_all_modules_for_project,
+    discover_all_modules_for_project_with_shadowed,
+)
 from specfact_cli.registry.module_installer import (
     REGISTRY_ID_FILE,
     USER_MODULES_ROOT,
@@ -187,7 +193,10 @@ def _normalize_project_repo(repo: Path | None) -> Path | None:
     if repo is None:
         return None
     repo_path = repo.resolve()
+    temp_root = Path(tempfile.gettempdir()).resolve()
     for candidate in [repo_path, *repo_path.parents]:
+        if candidate == temp_root and candidate != repo_path:
+            return repo_path
         if (candidate / ".git").exists():
             return candidate
     return repo_path
@@ -1062,6 +1071,107 @@ def _print_bundled_available_table(available: list[ModulePackageMetadata]) -> No
     console.print("[dim]Install bundled modules into project scope: specfact module init --scope project[/dim]")
 
 
+def _doctor_entry_matches(entry: DiscoveredModule, module_id: str | None) -> bool:
+    if module_id is None:
+        return True
+    requested = module_id.strip()
+    if not requested:
+        return True
+    discovered_id = entry.metadata.name
+    if requested == discovered_id:
+        return True
+    if "/" in requested:
+        return False
+    return requested.rsplit("/", 1)[-1] == discovered_id.rsplit("/", 1)[-1]
+
+
+def _doctor_dev_roots() -> list[tuple[str, str]]:
+    roots: list[tuple[str, str]] = []
+    for env_name in ("SPECFACT_MODULES_REPO", "SPECFACT_CLI_MODULES_REPO"):
+        value = os.environ.get(env_name, "").strip()
+        if value:
+            roots.append((env_name, value))
+    for raw_root in os.environ.get("SPECFACT_MODULES_ROOTS", "").split(os.pathsep):
+        value = raw_root.strip()
+        if value:
+            roots.append(("SPECFACT_MODULES_ROOTS", value))
+    return roots
+
+
+def _doctor_status(
+    entry: DiscoveredModule,
+    seen_by_module_id: set[str],
+    enabled_state: dict[str, dict[str, Any]],
+) -> str:
+    module_id = entry.metadata.name
+    if module_id in seen_by_module_id:
+        return "shadowed"
+    seen_by_module_id.add(module_id)
+    if enabled_state.get(module_id, {}).get("enabled", True) is False:
+        return "disabled"
+    return "effective"
+
+
+def _print_doctor_recovery(entries: list[tuple[DiscoveredModule, str]]) -> None:
+    for entry, status in entries:
+        if status != "shadowed" or entry.source != "user":
+            continue
+        console.print(f"[yellow]Recovery:[/yellow] specfact module uninstall {entry.metadata.name} --scope user")
+
+
+@app.command(name="doctor")
+@beartype
+@require(_module_id_optional_nonempty, "module_id must be non-empty if provided")
+def doctor(
+    module_id: str | None = typer.Argument(None, help="Optional module id to inspect"),
+    repo: Path | None = typer.Option(None, "--repo", help="Repository path for project scope (default: current dir)"),
+) -> None:
+    """Diagnose module scope, shadowing, and development source roots."""
+    repo_path = (repo or Path.cwd()).resolve()
+    discovered = [
+        entry
+        for entry in discover_all_modules_for_project_with_shadowed(repo_path)
+        if _doctor_entry_matches(entry, module_id)
+    ]
+    if not discovered:
+        console.print("[yellow]No matching modules discovered.[/yellow]")
+    else:
+        state = read_modules_state()
+        seen_by_module_id: set[str] = set()
+        rows: list[tuple[DiscoveredModule, str]] = []
+        table = Table(title="Module Doctor")
+        table.add_column("Module", style="cyan")
+        table.add_column("Version", style="magenta")
+        table.add_column("Status", style="yellow")
+        table.add_column("Origin", style="blue")
+        table.add_column("Enabled", style="green")
+        table.add_column("Path", overflow="fold")
+        for entry in discovered:
+            status = _doctor_status(entry, seen_by_module_id, state)
+            enabled = state.get(entry.metadata.name, {}).get("enabled", True) is not False
+            rows.append((entry, status))
+            table.add_row(
+                entry.metadata.name,
+                entry.metadata.version,
+                status,
+                entry.source,
+                "yes" if enabled else "no",
+                str(entry.package_dir),
+            )
+        console.print(table)
+        _print_doctor_recovery(rows)
+
+    dev_roots = _doctor_dev_roots()
+    if not dev_roots:
+        return
+    dev_table = Table(title="Development Source Roots")
+    dev_table.add_column("Source", style="cyan")
+    dev_table.add_column("Path", overflow="fold")
+    for source, path in dev_roots:
+        dev_table.add_row(source, path)
+    console.print(dev_table)
+
+
 @app.command(name="list")
 @beartype
 @require(