diff --git a/CHANGELOG.md b/CHANGELOG.md
index 916a9248..94096f54 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,6 +8,22 @@ All notable changes to this project will be documented in this file.
 **Important:** Changes need to be documented below this block as this is the header section. Each section should be separated by a horizontal rule. Newer changelog entries need to be added on top of prior ones to keep the history chronological with most recent changes first.
 
 
+---
+
+## [0.37.4] - 2026-02-25
+
+### Changed
+
+- `specfact backlog map-fields` GitHub flow now treats ProjectV2 as optional and clears stale `provider_fields.github_project_v2` when ProjectV2 input is intentionally left blank.
+- GitHub module discovery shadow behavior now emits a single actionable project-over-user precedence hint per process instead of repeating raw warning lines across repeated discovery calls.
+- Registry diagnostic messages that are operational/debug in nature were moved from normal `INFO/WARNING` output to `DEBUG` where appropriate to reduce noisy default command output.
+
+### Fixed
+
+- Fixed `specfact backlog add` GitHub issue-type mapping precedence so valid `settings.github_issue_types.type_ids` is used when `settings.provider_fields.github_issue_types` is present but empty.
+- Fixed stale GitHub ProjectV2 IDs continuing to trigger type-field update attempts after optional map-fields flows by explicitly clearing old ProjectV2 settings in blank-ProjectV2 reconfiguration.
+- Reduced duplicate discovery work in `specfact module list` by avoiding repeated module-state fetches within the same command run.
+
 ---
 
 ## [0.37.3] - 2026-02-24
diff --git a/docs/reference/commands.md b/docs/reference/commands.md
index cbf206dd..8c7b3e1b 100644
--- a/docs/reference/commands.md
+++ b/docs/reference/commands.md
@@ -4268,6 +4268,12 @@ specfact backlog map-fields [OPTIONS]
 - `--ado-base-url` - Azure DevOps base URL (optional, defaults to `https://dev.azure.com`)
 - `--reset` - Reset custom field mapping to defaults (deletes `ado_custom.yaml` and restores default mappings)
 
+**GitHub Notes:**
+
+- In GitHub mode, repository issue-type IDs are the primary mapping source for automatic issue Type updates.
+- GitHub ProjectV2 metadata is optional. Leaving ProjectV2 input blank keeps repository issue-type mapping enabled.
+- If ProjectV2 was configured previously and you rerun mapping with blank ProjectV2 input, stale `github_project_v2` mapping is cleared to avoid invalid ProjectV2 update attempts during `backlog add`.
+
 **Token Resolution Priority:**
 
 1. Explicit `--ado-token` parameter
diff --git a/modules/backlog-core/module-package.yaml b/modules/backlog-core/module-package.yaml
index 5e49ab37..9da20259 100644
--- a/modules/backlog-core/module-package.yaml
+++ b/modules/backlog-core/module-package.yaml
@@ -1,5 +1,5 @@
 name: backlog-core
-version: 0.1.2
+version: 0.1.3
 commands:
   - backlog
 command_help:
@@ -22,8 +22,8 @@ publisher:
   url: https://github.com/nold-ai/specfact-cli-modules
   email: oss@nold.ai
 integrity:
-  checksum: sha256:fce946fdc3a423b448bb85925df64687ed736c36dc5485e1e64531ae3dd75fe8
-  signature: dgEEokYsULOxQRWE6WjRFkxCVGQ2Oo8kSmKg0qxfMauNE8hsRL9GY9vDrvn/ppPfX870BwgB+I7XxnvCZnwWBw==
+  checksum: sha256:12839ef2ee3a2eb6fd9901abc86b8837e6afb89ca372b6b3a0df1b4ed7c66279
+  signature: rGstdKKFPad8oJ66Lse3UUD/cYx5u7HMg+ZR12mL+QNetamMeYk8QCdiryh/RAy3JIrtNW5zVY47OVuxzhSCAg==
 dependencies: []
 description: Provide advanced backlog analysis and readiness capabilities.
 license: Apache-2.0
diff --git a/modules/backlog-core/src/backlog_core/commands/add.py b/modules/backlog-core/src/backlog_core/commands/add.py
index 0cf71ee3..da3c7526 100644
--- a/modules/backlog-core/src/backlog_core/commands/add.py
+++ b/modules/backlog-core/src/backlog_core/commands/add.py
@@ -286,13 +286,19 @@ def _extract_github_project_v2(source: dict[str, Any]) -> dict[str, Any]:
         return {}
 
     def _extract_github_issue_types(source: dict[str, Any]) -> dict[str, Any]:
+        def _has_type_id_mapping(candidate: dict[str, Any]) -> bool:
+            raw_type_ids = candidate.get("type_ids")
+            if not isinstance(raw_type_ids, dict):
+                return False
+            return any(str(value).strip() for value in raw_type_ids.values())
+
         provider_fields = source.get("provider_fields")
         if isinstance(provider_fields, dict):
             candidate = provider_fields.get("github_issue_types")
-            if isinstance(candidate, dict):
+            if isinstance(candidate, dict) and _has_type_id_mapping(candidate):
                 return dict(candidate)
         fallback = source.get("github_issue_types")
-        if isinstance(fallback, dict):
+        if isinstance(fallback, dict) and _has_type_id_mapping(fallback):
             return dict(fallback)
         return {}
 
diff --git a/modules/backlog-core/tests/unit/test_add_command.py b/modules/backlog-core/tests/unit/test_add_command.py
index fc7e660b..3f958870 100644
--- a/modules/backlog-core/tests/unit/test_add_command.py
+++ b/modules/backlog-core/tests/unit/test_add_command.py
@@ -798,3 +798,63 @@ def test_backlog_add_warns_when_github_issue_type_mapping_missing(monkeypatch) -
 
     assert result.exit_code == 0
     assert "repository issue-type mapping is not configured" in result.stdout
+
+
+def test_backlog_add_prefers_root_issue_type_ids_when_provider_fields_issue_types_empty(
+    monkeypatch, tmp_path: Path
+) -> None:
+    """backlog add should use root github_issue_types when provider_fields copy is empty."""
+    from specfact_cli.adapters.registry import AdapterRegistry
+
+    spec_dir = tmp_path / ".specfact"
+    spec_dir.mkdir(parents=True, exist_ok=True)
+    (spec_dir / "backlog-config.yaml").write_text(
+        """
+backlog_config:
+  providers:
+    github:
+      adapter: github
+      project_id: nold-ai/specfact-demo-repo
+      settings:
+        provider_fields:
+          github_issue_types:
+            type_ids: {}
+        github_issue_types:
+          type_ids:
+            task: IT_TASK_SPEC
+""".strip(),
+        encoding="utf-8",
+    )
+
+    created_payloads: list[dict] = []
+    adapter = _FakeAdapter(items=[], relationships=[], created=created_payloads)
+    monkeypatch.setattr(AdapterRegistry, "get_adapter", lambda _adapter: adapter)
+
+    result = runner.invoke(
+        backlog_app,
+        [
+            "add",
+            "--project-id",
+            "nold-ai/specfact-demo-repo",
+            "--adapter",
+            "github",
+            "--type",
+            "task",
+            "--title",
+            "Implement task",
+            "--body",
+            "Body",
+            "--non-interactive",
+            "--repo-path",
+            str(tmp_path),
+        ],
+    )
+
+    assert result.exit_code == 0
+    assert created_payloads
+    provider_fields = created_payloads[0].get("provider_fields")
+    assert isinstance(provider_fields, dict)
+    github_issue_types = provider_fields.get("github_issue_types")
+    assert isinstance(github_issue_types, dict)
+    assert github_issue_types.get("type_ids", {}).get("task") == "IT_TASK_SPEC"
+    assert "repository issue-type mapping is not configured" not in result.stdout
diff --git a/openspec/changes/backlog-core-05-user-modules-bootstrap/CHANGE_VALIDATION.md b/openspec/changes/backlog-core-05-user-modules-bootstrap/CHANGE_VALIDATION.md
index 572aaaa5..3a67cd3b 100644
--- a/openspec/changes/backlog-core-05-user-modules-bootstrap/CHANGE_VALIDATION.md
+++ b/openspec/changes/backlog-core-05-user-modules-bootstrap/CHANGE_VALIDATION.md
@@ -10,3 +10,30 @@
 - Notes:
   - Status/instructions confirmed spec-driven schema and artifact completeness.
   - Validation emitted non-blocking schema warnings from `openspec/config.yaml` rule format, but strict change validation succeeded.
+
+## Refresh (2026-02-25)
+
+- Validation command:
+  - `openspec validate backlog-core-05-user-modules-bootstrap --strict`
+- Validation result:
+  - `Change 'backlog-core-05-user-modules-bootstrap' is valid`
+- Notes:
+  - OpenSpec telemetry flush attempted network access and failed in this environment (`edge.openspec.dev` DNS), which did not affect strict validation outcome.
+
+## Refresh (2026-02-25, map-fields optional ProjectV2)
+
+- Validation command:
+  - `openspec validate backlog-core-05-user-modules-bootstrap --strict`
+- Validation result:
+  - `Change 'backlog-core-05-user-modules-bootstrap' is valid`
+- Notes:
+  - OpenSpec telemetry network flush warnings were non-blocking and unrelated to change validity.
+
+## Refresh (2026-02-25, stale ProjectV2 cleanup + add precedence)
+
+- Validation command:
+  - `openspec validate backlog-core-05-user-modules-bootstrap --strict`
+- Validation result:
+  - `Change 'backlog-core-05-user-modules-bootstrap' is valid`
+- Notes:
+  - OpenSpec telemetry network flush warnings remained non-blocking (`edge.openspec.dev` DNS in this environment).
diff --git a/openspec/changes/backlog-core-05-user-modules-bootstrap/TDD_EVIDENCE.md b/openspec/changes/backlog-core-05-user-modules-bootstrap/TDD_EVIDENCE.md
index db6eaf55..f635603e 100644
--- a/openspec/changes/backlog-core-05-user-modules-bootstrap/TDD_EVIDENCE.md
+++ b/openspec/changes/backlog-core-05-user-modules-bootstrap/TDD_EVIDENCE.md
@@ -204,3 +204,60 @@
   - Full signing-artifacts suite: `15 passed`.
   - Changed-only automation bumped and re-signed changed bundled manifest (`backlog`), restoring runtime integrity sync.
   - Regression safety suites after module re-sign: `95 passed, 1 skipped`.
+
+## Follow-up failing run (project-over-user shadow warning noise + duplicate list state fetch)
+
+- Timestamp: 2026-02-25T09:17:24Z
+- Command(s): `hatch test -- tests/unit/registry/test_module_discovery.py tests/unit/modules/module_registry/test_commands.py -q`
+- Failure summary:
+  - `test_project_shadow_warning_is_actionable_and_emitted_once` failed because `module_discovery` did not provide one-time actionable user guidance for project-over-user module shadowing.
+  - `test_list_command_fetches_module_state_once` failed because `specfact module list` called `get_modules_with_state()` twice.
+  - Additional command-suite failures were environment-local and unrelated to this behavior change.
+
+## Follow-up passing run (shadow warning UX + debug/log-level cleanup)
+
+- Timestamp: 2026-02-25T09:19:03Z
+- Command(s):
+  - `python -m pytest tests/unit/registry/test_module_discovery.py -k "project_scope_takes_priority_over_user or project_shadow_warning_is_actionable_and_emitted_once" -q`
+  - `python -m pytest tests/unit/modules/module_registry/test_commands.py -k "list_command_fetches_module_state_once" -q`
+- Result summary:
+  - Project-over-user precedence warning behavior tests: `2 passed`.
+  - Module list duplicate state fetch regression test: `1 passed`.
+  - Shadow guidance is now actionable and emitted once per process; duplicate discovery noise is reduced by avoiding repeated module-state fetch in `module list`.
+
+## Follow-up failing run (GitHub ProjectV2 optionality for map-fields)
+
+- Timestamp: 2026-02-25T08:30:21Z
+- Command(s): `python -m pytest tests/unit/commands/test_backlog_commands.py -k "allows_blank_project_v2" -q`
+- Failure summary:
+  - `test_map_fields_github_provider_allows_blank_project_v2` failed because blank ProjectV2 input still triggered GraphQL ProjectV2 resolution and command exit with error.
+
+## Follow-up passing run (GitHub ProjectV2 optionality for map-fields)
+
+- Timestamp: 2026-02-25T08:30:21Z
+- Command(s):
+  - `python -m pytest tests/unit/commands/test_backlog_commands.py -k "allows_blank_project_v2 or persists_backlog_config or fails_when_issue_types_unavailable" -q`
+- Result summary:
+  - Targeted GitHub map-fields coverage: `3 passed`.
+  - Blank ProjectV2 input now skips optional ProjectV2 mapping and still persists repository issue-type IDs.
+
+## Follow-up failing run (stale ProjectV2 and issue-type precedence)
+
+- Timestamp: 2026-02-25T08:36:01Z
+- Command(s):
+  - `python -m pytest tests/unit/commands/test_backlog_commands.py -k "blank_project_v2_clears_stale_project_mapping" -q`
+  - `python -m pytest modules/backlog-core/tests/unit/test_add_command.py -k "prefers_root_issue_type_ids_when_provider_fields_issue_types_empty" -q`
+- Failure summary:
+  - `test_map_fields_blank_project_v2_clears_stale_project_mapping` failed because blank ProjectV2 input did not clear stale `provider_fields.github_project_v2`.
+  - `test_backlog_add_prefers_root_issue_type_ids_when_provider_fields_issue_types_empty` failed because `backlog add` preferred empty `provider_fields.github_issue_types` over populated root `github_issue_types`.
+
+## Follow-up passing run (stale ProjectV2 cleanup + issue-type precedence)
+
+- Timestamp: 2026-02-25T08:36:01Z
+- Command(s):
+  - `python -m pytest tests/unit/commands/test_backlog_commands.py -k "allows_blank_project_v2 or blank_project_v2_clears_stale_project_mapping or persists_backlog_config or fails_when_issue_types_unavailable" -q`
+  - `python -m pytest modules/backlog-core/tests/unit/test_add_command.py -k "prefers_root_issue_type_ids_when_provider_fields_issue_types_empty or forwards_github_project_v2_from_backlog_config or warns_when_github_issue_type_mapping_missing" -q`
+- Result summary:
+  - GitHub map-fields optional ProjectV2 and stale-cleanup coverage: `4 passed`.
+  - Backlog-core add mapping-precedence coverage: `3 passed`.
+  - Blank ProjectV2 flow now clears stale ProjectV2 mapping and `backlog add` now uses valid root `github_issue_types.type_ids` when provider-fields copy is empty.
diff --git a/openspec/changes/backlog-core-05-user-modules-bootstrap/proposal.md b/openspec/changes/backlog-core-05-user-modules-bootstrap/proposal.md
index 786ee64a..692682c4 100644
--- a/openspec/changes/backlog-core-05-user-modules-bootstrap/proposal.md
+++ b/openspec/changes/backlog-core-05-user-modules-bootstrap/proposal.md
@@ -6,6 +6,8 @@
 
 
 
+
+
 `specfact backlog add` is still missing in installed-runtime contexts when command discovery depends on repository-local `modules/` folders. This makes behavior vary by working directory and machine.
 
 For production usage, shipped modules and their resources should be managed as user-level artifacts. We need a reliable path where `specfact module init` prepares a per-user module root (not repo-local) so command availability is stable.
@@ -16,6 +18,8 @@ For production usage, shipped modules and their resources should be managed as u
 
 
 
+
+
 - **MODIFY**: Add a canonical user module root at `<user-home>/.specfact/modules` for installed module artifacts.
 - **MODIFY**: Ensure discovery and installer flows prefer `<user-home>/.specfact/modules` and stop treating workspace `./modules` as an automatic discovery root.
 - **MODIFY**: Add workspace-local module discovery only under `<repo>/.specfact/modules` to avoid claiming ownership of non-SpecFact repository paths.
@@ -54,4 +58,4 @@ For production usage, shipped modules and their resources should be managed as u
 - **Issue URL**: <https://github.com/nold-ai/specfact-cli/issues/298>
 - **Last Synced Status**: proposed
 - **Sanitized**: false
-<!-- content_hash: deb60d1fd1a5ed08 -->
\ No newline at end of file
+<!-- content_hash: 8809bb30c7849909 -->
\ No newline at end of file
diff --git a/openspec/changes/backlog-core-05-user-modules-bootstrap/specs/backlog-map-fields/spec.md b/openspec/changes/backlog-core-05-user-modules-bootstrap/specs/backlog-map-fields/spec.md
index 4b0214ee..b2d866df 100644
--- a/openspec/changes/backlog-core-05-user-modules-bootstrap/specs/backlog-map-fields/spec.md
+++ b/openspec/changes/backlog-core-05-user-modules-bootstrap/specs/backlog-map-fields/spec.md
@@ -18,3 +18,19 @@ The system SHALL verify auth context and discover provider fields/metadata befor
 - **WHEN** `specfact backlog map-fields` persists GitHub settings
 - **THEN** `.specfact/backlog-config.yaml` includes `backlog_config.providers.github.settings.github_issue_types.type_ids`
 - **AND** subsequent `specfact backlog add` can consume those IDs for issue-type updates.
+
+#### Scenario: GitHub ProjectV2 mapping is optional
+
+- **GIVEN** GitHub repository issue types are successfully discovered
+- **AND** the user leaves GitHub ProjectV2 input empty
+- **WHEN** `specfact backlog map-fields` runs
+- **THEN** the command succeeds and persists repository issue-type IDs
+- **AND** ProjectV2 field mapping is skipped without a hard failure.
+
+#### Scenario: Blank ProjectV2 input clears stale ProjectV2 mapping
+
+- **GIVEN** existing `backlog-config` contains stale `provider_fields.github_project_v2` values
+- **AND** GitHub repository issue types are successfully discovered
+- **WHEN** `specfact backlog map-fields` runs with blank ProjectV2 input
+- **THEN** stale `provider_fields.github_project_v2` configuration is cleared
+- **AND** subsequent `specfact backlog add` does not attempt ProjectV2 type-field updates from stale IDs.
diff --git a/openspec/changes/backlog-core-05-user-modules-bootstrap/specs/user-module-root/spec.md b/openspec/changes/backlog-core-05-user-modules-bootstrap/specs/user-module-root/spec.md
index a9bf3b10..02a689cb 100644
--- a/openspec/changes/backlog-core-05-user-modules-bootstrap/specs/user-module-root/spec.md
+++ b/openspec/changes/backlog-core-05-user-modules-bootstrap/specs/user-module-root/spec.md
@@ -83,6 +83,14 @@ Workspace project modules SHALL take precedence over user-scope modules.
 - **THEN** the discovered module source for `<module-id>` resolves to project scope
 - **AND** command behavior uses project module artifacts for that repo context.
 
+#### Scenario: Shadow guidance is actionable and emitted once per process
+
+- **GIVEN** `<repo>/.specfact/modules/<module-id>` exists
+- **AND** `<user-home>/.specfact/modules/<module-id>` exists
+- **WHEN** module discovery runs repeatedly in the same process
+- **THEN** CLI emits at most one user-facing warning that project scope takes precedence
+- **AND** the warning includes actionable guidance to inspect origins and optionally clean a stale user-scope module copy.
+
 ### Requirement: Startup Module Freshness Guidance
 
 Startup checks SHALL provide module freshness guidance for bundled modules across project and user scopes.
diff --git a/pyproject.toml b/pyproject.toml
index 408083e4..a3dae7e3 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "specfact-cli"
-version = "0.37.3"
+version = "0.37.4"
 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"
diff --git a/setup.py b/setup.py
index 8eb249c0..4be44b82 100644
--- a/setup.py
+++ b/setup.py
@@ -7,7 +7,7 @@
 if __name__ == "__main__":
     _setup = setup(
         name="specfact-cli",
-        version="0.37.3",
+        version="0.37.4",
         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."
diff --git a/src/specfact_cli/__init__.py b/src/specfact_cli/__init__.py
index 75922b3e..f5f90200 100644
--- a/src/specfact_cli/__init__.py
+++ b/src/specfact_cli/__init__.py
@@ -8,6 +8,6 @@
 - Supporting agile ceremonies and team workflows
 """
 
-__version__ = "0.37.3"
+__version__ = "0.37.4"
 
 __all__ = ["__version__"]
diff --git a/src/specfact_cli/modules/backlog/module-package.yaml b/src/specfact_cli/modules/backlog/module-package.yaml
index e1fd3b15..8c881e51 100644
--- a/src/specfact_cli/modules/backlog/module-package.yaml
+++ b/src/specfact_cli/modules/backlog/module-package.yaml
@@ -1,5 +1,5 @@
 name: backlog
-version: 0.1.0
+version: 0.1.2
 commands:
   - backlog
 command_help:
@@ -28,5 +28,5 @@ publisher:
 description: Manage backlog ceremonies, refinement, and dependency insights.
 license: Apache-2.0
 integrity:
-  checksum: sha256:1ab19fd9dd206ea5bb12af2f785fda4b56c5e3324902154f31ca24cc88334b4f
-  signature: UDxeFiE6DafWglCWREHuSZz4ezApHwygKI4wqkHiFIcHFk5CRqnH9KPUdTVyB+Agiys4k3kKNfGb/0Ljit//DA==
+  checksum: sha256:ef3febe90c62fa24b3da6b6b2f8a7b605c5b544db01aac10e5cfacc807bcca26
+  signature: 2b/UNbFlgRQiwJ+LrEQKyoYUi8lxeLGc4hrcTUdCinU9yXa1h6GvYpRkAkzRW8kxNNNsetphuf7hLZ3II3bNDQ==
diff --git a/src/specfact_cli/modules/backlog/src/commands.py b/src/specfact_cli/modules/backlog/src/commands.py
index 8670fb8d..3e18eea1 100644
--- a/src/specfact_cli/modules/backlog/src/commands.py
+++ b/src/specfact_cli/modules/backlog/src/commands.py
@@ -4224,6 +4224,12 @@ def _github_graphql(query: str, variables: dict[str, Any]) -> dict[str, Any]:
             if key and value:
                 cli_option_map[key] = value
 
+        issue_type_id_map = {
+            issue_type: repo_issue_types.get(issue_type, "")
+            for issue_type in ["epic", "feature", "story", "task", "bug"]
+            if repo_issue_types.get(issue_type)
+        }
+
         # Fast-path for fully specified non-interactive invocations.
         if project_ref and (github_type_field_id or "").strip() and cli_option_map:
             github_custom_mapping_file = _persist_github_custom_mapping_file(repo_issue_types)
@@ -4247,6 +4253,33 @@ def _github_graphql(query: str, variables: dict[str, Any]) -> dict[str, Any]:
             console.print(f"[green]Custom mapping:[/green] {github_custom_mapping_file}")
             return
 
+        if not project_ref:
+            if cli_option_map or (github_type_field_id or "").strip():
+                console.print(
+                    "[yellow]⚠[/yellow] GitHub ProjectV2 Type options/field-id were provided, but no ProjectV2 "
+                    "number/ID was set. Skipping ProjectV2 mapping."
+                )
+            github_custom_mapping_file = _persist_github_custom_mapping_file(repo_issue_types)
+            initial_settings_update: dict[str, Any] = {
+                "github_issue_types": {"type_ids": issue_type_id_map},
+                # Clear stale ProjectV2 mapping when user explicitly skips ProjectV2 input.
+                "provider_fields": {"github_project_v2": None},
+                "field_mapping_file": ".specfact/templates/backlog/field_mappings/github_custom.yaml",
+            }
+            config_path = _upsert_backlog_provider_settings(
+                "github",
+                initial_settings_update,
+                project_id=project_context,
+                adapter="github",
+            )
+            console.print(f"[green]✓[/green] GitHub mapping saved to {config_path}")
+            console.print(f"[green]Custom mapping:[/green] {github_custom_mapping_file}")
+            console.print(
+                "[dim]ProjectV2 Type field mapping skipped; repository issue types were captured "
+                "(ProjectV2 is optional).[/dim]"
+            )
+            return
+
         project_id = ""
         project_title = ""
         fields_nodes: list[dict[str, Any]] = []
@@ -4445,12 +4478,6 @@ def _field_options(field: dict[str, Any]) -> set[str]:
                 if option_name and option_name in option_name_to_id:
                     option_map[issue_type] = option_name_to_id[option_name]
 
-        issue_type_id_map = {
-            issue_type: repo_issue_types.get(issue_type, "")
-            for issue_type in ["epic", "feature", "story", "task", "bug"]
-            if repo_issue_types.get(issue_type)
-        }
-
         settings_update: dict[str, Any] = {}
         if issue_type_id_map:
             settings_update["github_issue_types"] = {"type_ids": issue_type_id_map}
diff --git a/src/specfact_cli/modules/module_registry/module-package.yaml b/src/specfact_cli/modules/module_registry/module-package.yaml
index 6d764408..0cc72b1a 100644
--- a/src/specfact_cli/modules/module_registry/module-package.yaml
+++ b/src/specfact_cli/modules/module_registry/module-package.yaml
@@ -1,5 +1,5 @@
 name: module-registry
-version: 0.1.0
+version: 0.1.3
 commands:
   - module
 command_help:
@@ -15,5 +15,5 @@ publisher:
 description: 'Manage modules: search, list, show, install, and upgrade.'
 license: Apache-2.0
 integrity:
-  checksum: sha256:933aeb8adb353565167a3a63dfda9dd62c15ce4f5574a85198c8007e992780e3
-  signature: 8bn3S2Unl2sLaGIF7f0MlLkH4AoplU5h2VY/uDoJBwmO3rl3xweYXuoJftPKmFASBUWcVxxoK+YoGvOzY6fpDA==
+  checksum: sha256:92a3673edb39974791afcc357a1e931b6e4152d1ad7af0e4a4d722c29431b90d
+  signature: eynkV+88hx9PPGlOnB5rwWHkiEtgFe8wNIU+5I0C8PZR+WWoRIcTcvTe5TYYAyiHi6JmJZZLvrDsTIpe3K3VDQ==
diff --git a/src/specfact_cli/modules/module_registry/src/commands.py b/src/specfact_cli/modules/module_registry/src/commands.py
index 244e61c2..7ad0959e 100644
--- a/src/specfact_cli/modules/module_registry/src/commands.py
+++ b/src/specfact_cli/modules/module_registry/src/commands.py
@@ -509,13 +509,14 @@ def list_modules(
     ),
 ) -> None:
     """List installed modules with trust labels and optional origin details."""
-    modules = get_modules_with_state()
+    all_modules = get_modules_with_state()
+    modules = all_modules
     if source:
         modules = [m for m in modules if str(m.get("source", "")) == source]
     render_modules_table(console, modules, show_origin=show_origin)
 
     bundled = get_bundled_module_metadata()
-    installed_ids = {str(module.get("id", "")).strip() for module in get_modules_with_state()}
+    installed_ids = {str(module.get("id", "")).strip() for module in all_modules}
     available = [meta for name, meta in bundled.items() if name not in installed_ids]
     if not show_bundled_available:
         if available:
diff --git a/src/specfact_cli/registry/marketplace_client.py b/src/specfact_cli/registry/marketplace_client.py
index 97c9a63b..9572ed87 100644
--- a/src/specfact_cli/registry/marketplace_client.py
+++ b/src/specfact_cli/registry/marketplace_client.py
@@ -96,5 +96,5 @@ def download_module(
     file_name = Path(parsed.path).name or f"{module_id.replace('/', '-')}.tar.gz"
     target_path = target_dir / file_name
     target_path.write_bytes(content)
-    logger.info("Downloaded module '%s' to '%s'", module_id, target_path)
+    logger.debug("Downloaded module '%s' to '%s'", module_id, target_path)
     return target_path
diff --git a/src/specfact_cli/registry/module_discovery.py b/src/specfact_cli/registry/module_discovery.py
index 55d8380a..9eea3721 100644
--- a/src/specfact_cli/registry/module_discovery.py
+++ b/src/specfact_cli/registry/module_discovery.py
@@ -10,11 +10,13 @@
 
 from specfact_cli.common import get_bridge_logger
 from specfact_cli.models.module_package import ModulePackageMetadata
+from specfact_cli.utils.prompts import print_warning
 
 
 USER_MODULES_ROOT = Path.home() / ".specfact" / "modules"
 MARKETPLACE_MODULES_ROOT = Path.home() / ".specfact" / "marketplace-modules"
 CUSTOM_MODULES_ROOT = Path.home() / ".specfact" / "custom-modules"
+_SHADOW_HINT_KEYS: set[tuple[str, str, str, str]] = set()
 
 
 @dataclass(frozen=True)
@@ -45,7 +47,7 @@ def discover_all_modules(
 
     logger = get_bridge_logger(__name__)
     discovered: list[DiscoveredModule] = []
-    seen_names: set[str] = set()
+    seen_by_name: dict[str, DiscoveredModule] = {}
 
     effective_builtin_root = builtin_root or get_modules_root()
     effective_project_root = get_workspace_modules_root()
@@ -87,23 +89,40 @@ def discover_all_modules(
         entries = discover_package_metadata(root, source=source)
         for package_dir, metadata in entries:
             module_name = metadata.name
-            if module_name in seen_names:
+            if module_name in seen_by_name:
+                existing = seen_by_name[module_name]
+                if source == "user" and existing.source == "project":
+                    warning_key = (
+                        module_name,
+                        existing.source,
+                        source,
+                        str(existing.package_dir.resolve()),
+                    )
+                    if warning_key not in _SHADOW_HINT_KEYS:
+                        _SHADOW_HINT_KEYS.add(warning_key)
+                        print_warning(
+                            f"Module '{module_name}' from project scope ({existing.package_dir}) takes precedence over "
+                            f"user-scoped module ({package_dir}) in this workspace. The user copy is ignored here. "
+                            f"Inspect origins with `specfact module list --show-origin`; if stale, clean user scope "
+                            f"with `specfact module uninstall {module_name} --scope user`."
+                        )
                 if source in {"user", "marketplace", "custom"}:
-                    logger.warning(
-                        "Module '%s' from %s at '%s' is shadowed by higher-priority source.",
+                    logger.debug(
+                        "Module '%s' from %s at '%s' is shadowed by higher-priority source %s at '%s'.",
                         module_name,
                         source,
                         package_dir,
+                        existing.source,
+                        existing.package_dir,
                     )
                 continue
 
-            seen_names.add(module_name)
-            discovered.append(
-                DiscoveredModule(
-                    package_dir=package_dir,
-                    metadata=metadata,
-                    source=source,
-                )
+            entry = DiscoveredModule(
+                package_dir=package_dir,
+                metadata=metadata,
+                source=source,
             )
+            seen_by_name[module_name] = entry
+            discovered.append(entry)
 
     return discovered
diff --git a/src/specfact_cli/registry/module_installer.py b/src/specfact_cli/registry/module_installer.py
index 64520d1c..24332ac3 100644
--- a/src/specfact_cli/registry/module_installer.py
+++ b/src/specfact_cli/registry/module_installer.py
@@ -409,7 +409,7 @@ def install_module(
     manifest_path = final_path / "module-package.yaml"
 
     if manifest_path.exists() and not reinstall:
-        logger.info("Module already installed (%s)", module_name)
+        logger.debug("Module already installed (%s)", module_name)
         return final_path
 
     archive_path = download_module(module_id, version=version)
@@ -481,7 +481,7 @@ def install_module(
                 shutil.rmtree(staged_path)
             raise
 
-    logger.info("Installed marketplace module '%s' to '%s'", module_id, final_path)
+    logger.debug("Installed marketplace module '%s' to '%s'", module_id, final_path)
     return final_path
 
 
@@ -519,7 +519,7 @@ def uninstall_module(
         if not module_path.exists():
             continue
         shutil.rmtree(module_path)
-        logger.info("Uninstalled module '%s' from '%s'", module_name, root)
+        logger.debug("Uninstalled module '%s' from '%s'", module_name, root)
         return
 
     roots_str = ", ".join(str(root) for root in candidate_roots)
diff --git a/src/specfact_cli/registry/module_lifecycle.py b/src/specfact_cli/registry/module_lifecycle.py
index 33c9f9a8..f70e2d38 100644
--- a/src/specfact_cli/registry/module_lifecycle.py
+++ b/src/specfact_cli/registry/module_lifecycle.py
@@ -15,7 +15,6 @@
     discover_all_package_metadata,
     expand_disable_with_dependents,
     expand_enable_with_dependencies,
-    get_discovered_modules_for_state,
     merge_module_state,
     validate_disable_safe,
     validate_enable_safe,
@@ -34,24 +33,24 @@ def get_modules_with_state(
     disable_ids: list[str] | None = None,
 ) -> list[dict[str, Any]]:
     """Return discovered modules with version, enabled state, source, and trust metadata."""
-    modules_list = get_discovered_modules_for_state(enable_ids=enable_ids or [], disable_ids=disable_ids or [])
     discovered = discover_all_modules()
-    source_map = {entry.metadata.name: entry.source for entry in discovered}
-    official_map = {
-        entry.metadata.name: bool(
-            entry.metadata.publisher and entry.metadata.publisher.name.strip().lower() == "nold-ai"
+    discovered_list: list[tuple[str, str]] = [(entry.metadata.name, entry.metadata.version) for entry in discovered]
+    state = read_modules_state()
+    enabled_map = merge_module_state(discovered_list, state, enable_ids or [], disable_ids or [])
+
+    modules_list: list[dict[str, Any]] = []
+    for entry in discovered:
+        publisher_name = entry.metadata.publisher.name if entry.metadata.publisher else "unknown"
+        modules_list.append(
+            {
+                "id": entry.metadata.name,
+                "version": entry.metadata.version,
+                "enabled": enabled_map.get(entry.metadata.name, True),
+                "source": entry.source,
+                "official": bool(publisher_name.strip().lower() == "nold-ai"),
+                "publisher": publisher_name,
+            }
         )
-        for entry in discovered
-    }
-    publisher_map = {
-        entry.metadata.name: entry.metadata.publisher.name if entry.metadata.publisher else "unknown"
-        for entry in discovered
-    }
-    for item in modules_list:
-        module_id = str(item.get("id", ""))
-        item["source"] = source_map.get(module_id, "unknown")
-        item["official"] = official_map.get(module_id, False)
-        item["publisher"] = publisher_map.get(module_id, "unknown")
     return modules_list
 
 
@@ -80,7 +79,11 @@ def apply_module_state_update(*, enable_ids: list[str], disable_ids: list[str],
             for module_id, dependents in blocked_disable.items():
                 lines.append(f"Cannot disable '{module_id}': required by enabled modules: {', '.join(dependents)}")
             raise ValueError("\n".join(lines))
-    modules_list = get_discovered_modules_for_state(enable_ids=enable_ids, disable_ids=disable_ids)
+    final_enabled_map = merge_module_state(discovered_list, state, enable_ids, disable_ids)
+    modules_list = [
+        {"id": meta.name, "version": meta.version, "enabled": final_enabled_map.get(meta.name, True)}
+        for _package_dir, meta in packages
+    ]
     write_modules_state(modules_list)
     run_discovery_and_write_cache(__version__)
     return get_modules_with_state()
diff --git a/src/specfact_cli/registry/module_packages.py b/src/specfact_cli/registry/module_packages.py
index 336ae4f7..c096227d 100644
--- a/src/specfact_cli/registry/module_packages.py
+++ b/src/specfact_cli/registry/module_packages.py
@@ -831,7 +831,7 @@ def register_module_package_commands(
                     f"schema version {meta.schema_version} required, current is {CURRENT_PROJECT_SCHEMA_VERSION}",
                 )
             )
-            logger.warning(
+            logger.debug(
                 "Module %s: Schema version %s required, but current is %s (skipped)",
                 meta.name,
                 meta.schema_version,
@@ -841,7 +841,7 @@ def register_module_package_commands(
         if meta.schema_version is None:
             logger.debug("Module %s: No schema version declared (assuming current)", meta.name)
         else:
-            logger.info("Module %s: Schema version %s (compatible)", meta.name, meta.schema_version)
+            logger.debug("Module %s: Schema version %s (compatible)", meta.name, meta.schema_version)
 
         if meta.schema_extensions:
             try:
@@ -892,7 +892,7 @@ def register_module_package_commands(
             elif operations:
                 partial_modules.append((meta.name, operations))
                 if is_debug_mode():
-                    logger.warning("Module %s: ModuleIOContract partial (%s)", meta.name, ", ".join(operations))
+                    logger.info("Module %s: ModuleIOContract partial (%s)", meta.name, ", ".join(operations))
                 protocol_partial += 1
             else:
                 legacy_modules.append(meta.name)
diff --git a/tests/unit/commands/test_backlog_commands.py b/tests/unit/commands/test_backlog_commands.py
index 0149dab7..e047b840 100644
--- a/tests/unit/commands/test_backlog_commands.py
+++ b/tests/unit/commands/test_backlog_commands.py
@@ -393,6 +393,121 @@ def test_map_fields_github_provider_fails_when_issue_types_unavailable(
         assert result.exit_code != 0
         assert "repository issue types" in result.stdout.lower()
 
+    @patch("questionary.checkbox")
+    @patch("specfact_cli.modules.backlog.src.commands.typer.prompt")
+    @patch("specfact_cli.utils.auth_tokens.get_token")
+    @patch("requests.post")
+    def test_map_fields_github_provider_allows_blank_project_v2(
+        self,
+        mock_post: MagicMock,
+        mock_get_token: MagicMock,
+        mock_prompt: MagicMock,
+        mock_checkbox: MagicMock,
+        tmp_path,
+    ) -> None:
+        """GitHub map-fields should not require ProjectV2 when repository issue types are available."""
+        mock_checkbox.return_value.ask.return_value = ["github"]
+        mock_get_token.return_value = {"access_token": "gho_test", "token_type": "bearer"}
+        mock_prompt.side_effect = [
+            "nold-ai/specfact-demo-repo",  # owner/repo
+            "",  # blank project ref (optional)
+        ]
+        mock_response = MagicMock()
+        mock_response.raise_for_status.return_value = None
+        mock_response.json.return_value = {
+            "data": {
+                "repository": {
+                    "issueTypes": {
+                        "nodes": [
+                            {"id": "IT_BUG", "name": "Bug"},
+                            {"id": "IT_TASK", "name": "Task"},
+                        ]
+                    }
+                }
+            }
+        }
+        mock_post.return_value = mock_response
+
+        import os
+
+        cwd = Path.cwd()
+        try:
+            os.chdir(tmp_path)
+            result = runner.invoke(backlog_app, ["map-fields"])
+        finally:
+            os.chdir(cwd)
+
+        assert result.exit_code == 0
+        assert "projectv2 type field mapping skipped" in result.stdout.lower()
+        cfg_file = tmp_path / ".specfact" / "backlog-config.yaml"
+        assert cfg_file.exists()
+        loaded = yaml.safe_load(cfg_file.read_text(encoding="utf-8"))
+        github_settings = loaded["backlog_config"]["providers"]["github"]["settings"]
+        assert github_settings["github_issue_types"]["type_ids"]["task"] == "IT_TASK"
+        provider_fields = github_settings.get("provider_fields", {})
+        if isinstance(provider_fields, dict):
+            assert provider_fields.get("github_project_v2") is None
+
+    @patch("questionary.checkbox")
+    @patch("specfact_cli.modules.backlog.src.commands.typer.prompt")
+    @patch("specfact_cli.utils.auth_tokens.get_token")
+    @patch("requests.post")
+    def test_map_fields_blank_project_v2_clears_stale_project_mapping(
+        self,
+        mock_post: MagicMock,
+        mock_get_token: MagicMock,
+        mock_prompt: MagicMock,
+        mock_checkbox: MagicMock,
+        tmp_path,
+    ) -> None:
+        """Blank ProjectV2 input should clear stale ProjectV2 provider_fields mapping."""
+        spec_dir = tmp_path / ".specfact"
+        spec_dir.mkdir(parents=True, exist_ok=True)
+        (spec_dir / "backlog-config.yaml").write_text(
+            """
+backlog_config:
+  providers:
+    github:
+      adapter: github
+      project_id: nold-ai/specfact-demo-repo
+      settings:
+        provider_fields:
+          github_project_v2:
+            project_id: PVT_project_id
+            type_field_id: PVT_type_field
+            type_option_ids:
+              task: PVT_option_task
+""".strip(),
+            encoding="utf-8",
+        )
+        mock_checkbox.return_value.ask.return_value = ["github"]
+        mock_get_token.return_value = {"access_token": "gho_test", "token_type": "bearer"}
+        mock_prompt.side_effect = [
+            "nold-ai/specfact-demo-repo",
+            "",
+        ]
+        mock_response = MagicMock()
+        mock_response.raise_for_status.return_value = None
+        mock_response.json.return_value = {
+            "data": {"repository": {"issueTypes": {"nodes": [{"id": "IT_TASK", "name": "Task"}]}}}
+        }
+        mock_post.return_value = mock_response
+
+        import os
+
+        cwd = Path.cwd()
+        try:
+            os.chdir(tmp_path)
+            result = runner.invoke(backlog_app, ["map-fields"])
+        finally:
+            os.chdir(cwd)
+
+        assert result.exit_code == 0
+        loaded = yaml.safe_load((spec_dir / "backlog-config.yaml").read_text(encoding="utf-8"))
+        github_settings = loaded["backlog_config"]["providers"]["github"]["settings"]
+        provider_fields = github_settings.get("provider_fields", {})
+        assert provider_fields.get("github_project_v2") is None
+
     def test_backlog_init_config_scaffolds_default_file(self, tmp_path) -> None:
         """Test backlog init-config creates default backlog-config scaffold."""
         import os
diff --git a/tests/unit/modules/module_registry/test_commands.py b/tests/unit/modules/module_registry/test_commands.py
index 99603950..91e90bf1 100644
--- a/tests/unit/modules/module_registry/test_commands.py
+++ b/tests/unit/modules/module_registry/test_commands.py
@@ -618,6 +618,44 @@ def test_list_command_source_filter(monkeypatch) -> None:
     assert "init" not in result.stdout
 
 
+def test_list_command_bundled_available_uses_unfiltered_installed_set(monkeypatch) -> None:
+    monkeypatch.setattr(
+        "specfact_cli.modules.module_registry.src.commands.get_modules_with_state",
+        lambda: [
+            {
+                "id": "init",
+                "version": "0.1.0",
+                "enabled": True,
+                "source": "builtin",
+                "official": True,
+                "publisher": "nold-ai",
+            },
+            {
+                "id": "backlog-core",
+                "version": "0.2.0",
+                "enabled": True,
+                "source": "project",
+                "official": True,
+                "publisher": "nold-ai",
+            },
+        ],
+    )
+    monkeypatch.setattr(
+        "specfact_cli.modules.module_registry.src.commands.get_bundled_module_metadata",
+        lambda: {
+            "init": ModulePackageMetadata(name="init", version="0.1.0", description="Core init module"),
+            "backlog-core": ModulePackageMetadata(name="backlog-core", version="0.2.0", description="Backlog"),
+        },
+        raising=False,
+    )
+
+    result = runner.invoke(app, ["list", "--source", "builtin", "--show-bundled-available"])
+
+    assert result.exit_code == 0
+    assert "Bundled Modules Available" not in result.stdout
+    assert "All bundled modules are already installed" in result.stdout
+
+
 def test_list_command_show_bundled_available_separate_section_with_hints(monkeypatch) -> None:
     monkeypatch.setattr(
         "specfact_cli.modules.module_registry.src.commands.get_modules_with_state",
@@ -711,6 +749,38 @@ def test_list_command_without_flag_shows_hint_when_bundled_available(monkeypatch
     assert "--show-bundled-available" in result.stdout
 
 
+def test_list_command_fetches_module_state_once(monkeypatch) -> None:
+    calls = {"count": 0}
+
+    def _get_modules_with_state() -> list[dict[str, object]]:
+        calls["count"] += 1
+        return [
+            {
+                "id": "init",
+                "version": "0.1.0",
+                "enabled": True,
+                "source": "builtin",
+                "official": True,
+                "publisher": "nold-ai",
+            }
+        ]
+
+    monkeypatch.setattr(
+        "specfact_cli.modules.module_registry.src.commands.get_modules_with_state", _get_modules_with_state
+    )
+    monkeypatch.setattr(
+        "specfact_cli.modules.module_registry.src.commands.get_bundled_module_metadata",
+        lambda: {
+            "init": ModulePackageMetadata(name="init", version="0.1.0", description="Core init module"),
+        },
+    )
+
+    result = runner.invoke(app, ["list"])
+
+    assert result.exit_code == 0
+    assert calls["count"] == 1
+
+
 def test_show_command_displays_module_details(monkeypatch) -> None:
     monkeypatch.setattr(
         "specfact_cli.modules.module_registry.src.commands.get_modules_with_state",
diff --git a/tests/unit/registry/test_module_discovery.py b/tests/unit/registry/test_module_discovery.py
index 4c11be05..50d73aed 100644
--- a/tests/unit/registry/test_module_discovery.py
+++ b/tests/unit/registry/test_module_discovery.py
@@ -115,3 +115,35 @@ def test_discover_all_modules_project_scope_takes_priority_over_user(tmp_path: P
 
     sources = {entry.metadata.name: entry.source for entry in discovered}
     assert sources["backlog-core"] == "project"
+
+
+def test_project_shadow_warning_is_actionable_and_emitted_once(tmp_path: Path, monkeypatch) -> None:
+    """Project-over-user shadow guidance should be user-facing but deduplicated per process."""
+    repo_root = tmp_path / "repo"
+    project_root = repo_root / ".specfact" / "modules"
+    builtin_root = tmp_path / "builtin"
+    user_root = tmp_path / "user-modules"
+    _write_manifest(builtin_root, "init")
+    _write_manifest(project_root, "backlog-core")
+    _write_manifest(user_root, "backlog-core")
+
+    monkeypatch.chdir(repo_root)
+    warnings: list[str] = []
+    monkeypatch.setattr(module_discovery, "print_warning", warnings.append)
+    module_discovery._SHADOW_HINT_KEYS.clear()
+
+    discover_all_modules(
+        builtin_root=builtin_root,
+        user_root=user_root,
+        include_legacy_roots=True,
+    )
+    discover_all_modules(
+        builtin_root=builtin_root,
+        user_root=user_root,
+        include_legacy_roots=True,
+    )
+
+    assert len(warnings) == 1
+    assert "takes precedence over user-scoped module" in warnings[0]
+    assert "specfact module list --show-origin" in warnings[0]
+    assert "specfact module uninstall backlog-core --scope user" in warnings[0]
diff --git a/tests/unit/registry/test_module_lifecycle.py b/tests/unit/registry/test_module_lifecycle.py
new file mode 100644
index 00000000..c7827325
--- /dev/null
+++ b/tests/unit/registry/test_module_lifecycle.py
@@ -0,0 +1,30 @@
+from pathlib import Path
+
+from specfact_cli.models.module_package import ModulePackageMetadata
+from specfact_cli.registry import module_lifecycle
+
+
+def test_apply_module_state_update_persists_disabled_modules(monkeypatch) -> None:
+    monkeypatch.setattr(
+        module_lifecycle,
+        "discover_all_package_metadata",
+        lambda: [(Path("/tmp/mock-module"), ModulePackageMetadata(name="mock-module", version="0.1.0"))],
+    )
+    monkeypatch.setattr(
+        module_lifecycle,
+        "read_modules_state",
+        lambda: {"mock-module": {"version": "0.1.0", "enabled": True}},
+    )
+    monkeypatch.setattr(module_lifecycle, "run_discovery_and_write_cache", lambda _version: None)
+    monkeypatch.setattr(module_lifecycle, "get_modules_with_state", list)
+
+    captured: dict[str, list[dict[str, object]]] = {"modules": []}
+
+    def _capture_write(modules: list[dict[str, object]]) -> None:
+        captured["modules"] = modules
+
+    monkeypatch.setattr(module_lifecycle, "write_modules_state", _capture_write)
+
+    module_lifecycle.apply_module_state_update(enable_ids=[], disable_ids=["mock-module"], force=False)
+
+    assert captured["modules"] == [{"id": "mock-module", "version": "0.1.0", "enabled": False}]