diff --git a/docs/adapters/azuredevops.md b/docs/adapters/azuredevops.md
index 142ae04..8529e34 100644
--- a/docs/adapters/azuredevops.md
+++ b/docs/adapters/azuredevops.md
@@ -187,7 +187,7 @@ adapter = AdoAdapter(
 
 ### Error diagnostics (PATCH failures)
 
-When a work item PATCH fails (e.g. HTTP 400 during backlog refine or status update), the CLI shows the ADO error message and a hint in the console. With `--debug`, the log includes the ADO response snippet and the JSON Patch paths attempted so you can identify the failing field. See [Debug Logging – Examining ADO API Errors](../reference/debug-logging.md#examining-ado-api-errors) and [Troubleshooting – Backlog refine or work item PATCH fails (400/422)](../guides/troubleshooting.md#backlog-refine-or-work-item-patch-fails-400422).
+When a work item PATCH fails (e.g. HTTP 400 during backlog refine or status update), the CLI shows the ADO error message and a hint in the console. With `--debug`, the log includes the ADO response snippet and the JSON Patch paths attempted so you can identify the failing field. See [Debug Logging – Examining ADO API Errors](https://docs.specfact.io/core-cli/debug-logging/#examining-ado-api-errors) and [Troubleshooting – Backlog refine or work item PATCH fails (400/422)](../guides/troubleshooting.md#backlog-refine-or-work-item-patch-fails-400422).
 
 ## Usage Examples
 
diff --git a/docs/guides/agile-scrum-workflows.md b/docs/guides/agile-scrum-workflows.md
index 9ddc88e..5039185 100644
--- a/docs/guides/agile-scrum-workflows.md
+++ b/docs/guides/agile-scrum-workflows.md
@@ -1046,5 +1046,5 @@ If template rendering fails:
 ## Related Documentation
 
 - [Command Reference - Project Commands](../reference/commands.md#project---project-bundle-management) - Complete command documentation including `project merge` and `project resolve-conflict`
-- [Project Bundle Structure](../reference/directory-structure.md) - Project bundle organization
+- [Project Bundle Structure](https://docs.specfact.io/reference/directory-structure/) - Project bundle organization (core CLI docs)
 - See [Project Commands](../reference/commands.md#project---project-bundle-management) for template customization options
diff --git a/docs/reference/README.md b/docs/reference/README.md
index 2a22435..399e674 100644
--- a/docs/reference/README.md
+++ b/docs/reference/README.md
@@ -19,12 +19,12 @@ Complete technical reference for the official modules site and bundle-owned work
 - **[Command Syntax Policy](command-syntax-policy.md)** - Source-of-truth argument syntax conventions for docs
 - **[Authentication](authentication.md)** - Device code auth flows and token storage
 - **[Architecture](architecture.md)** - Technical design, module structure, and internals
-- **[Debug Logging](debug-logging.md)** - Where and what is logged when using `--debug`
+- **[Debug Logging](https://docs.specfact.io/core-cli/debug-logging/)** - Where and what is logged when using `--debug` (core CLI docs)
 - **[Operational Modes](modes.md)** - CI/CD vs CoPilot modes
 - **[Specmatic API](specmatic.md)** - Specmatic integration API reference (functions, classes, integration points)
 - **[Telemetry](telemetry.md)** - Opt-in analytics and privacy guarantees
-- **[Feature Keys](feature-keys.md)** - Key normalization and formats
-- **[Directory Structure](directory-structure.md)** - Project structure and organization
+- **[Feature Keys](https://docs.specfact.io/reference/feature-keys/)** - Key normalization and formats (core CLI docs)
+- **[Directory Structure](https://docs.specfact.io/reference/directory-structure/)** - Project structure and organization (core CLI docs)
 - **[Schema Versioning](schema-versioning.md)** - Bundle schema versions and backward compatibility (v1.0, v1.1)
 - **[Module Security](module-security.md)** - Marketplace/module integrity and publisher metadata
 - **[Module Categories](module-categories.md)** - Category grouping model, canonical module assignments, bundles, and first-run profiles
diff --git a/docs/reference/architecture.md b/docs/reference/architecture.md
index 8403805..da4e46b 100644
--- a/docs/reference/architecture.md
+++ b/docs/reference/architecture.md
@@ -161,6 +161,6 @@ Formal ADR pages are not yet published on the modules docs site. The current arc
 
 ## Related Docs
 
-- [Directory Structure](directory-structure.md)
+- [Directory Structure](https://docs.specfact.io/reference/directory-structure/) (core CLI docs)
 - [Module Development Guide](/authoring/module-development/)
 - [Adapter Development Guide](/authoring/adapter-development/)
diff --git a/docs/reference/schema-versioning.md b/docs/reference/schema-versioning.md
index 010f1e9..2a12c6b 100644
--- a/docs/reference/schema-versioning.md
+++ b/docs/reference/schema-versioning.md
@@ -178,4 +178,4 @@ schema_metadata:
 
 - [Architecture - Change Tracking Models](../reference/architecture.md#change-tracking-models-v11-schema) - Technical details
 - [Architecture - Bridge Adapter Interface](../reference/architecture.md#bridge-adapter-interface) - Adapter implementation guide
-- [Directory Structure](directory-structure.md) - Bundle file organization
+- [Directory Structure](https://docs.specfact.io/reference/directory-structure/) - Bundle file organization (core CLI docs)
diff --git a/scripts/check-docs-commands.py b/scripts/check-docs-commands.py
index 8cb7741..ef7cc07 100755
--- a/scripts/check-docs-commands.py
+++ b/scripts/check-docs-commands.py
@@ -18,7 +18,16 @@
 REPO_ROOT = Path(__file__).resolve().parents[1]
 DOCS_ROOT = REPO_ROOT / "docs"
 CORE_DOCS_HOST = "docs.specfact.io"
-ALLOWED_CORE_DOCS_ROUTES = frozenset({"/", "/reference/documentation-url-contract/"})
+ALLOWED_CORE_DOCS_ROUTES = frozenset(
+    {
+        "/",
+        "/reference/documentation-url-contract/",
+        # Core-owned reference / guides linked from modules docs (see specfact-cli docs/ permalinks)
+        "/core-cli/debug-logging/",
+        "/reference/directory-structure/",
+        "/reference/feature-keys/",
+    }
+)
 CORE_COMMAND_PREFIXES = frozenset(
     {
         ("specfact",),
diff --git a/tests/unit/test_check_docs_commands_script.py b/tests/unit/test_check_docs_commands_script.py
index 04dfa0b..0b4de63 100644
--- a/tests/unit/test_check_docs_commands_script.py
+++ b/tests/unit/test_check_docs_commands_script.py
@@ -115,6 +115,23 @@ def test_validate_core_docs_links_rejects_unknown_route(tmp_path: Path) -> None:
     assert "missing/page" in findings[0].message
 
 
+def test_validate_core_docs_links_allows_core_handoff_routes(tmp_path: Path) -> None:
+    """Handoff URLs used in modules docs must stay in ALLOWED_CORE_DOCS_ROUTES (see scripts/check-docs-commands.py)."""
+    script = _load_script()
+    doc_path = tmp_path / "handoff.md"
+    doc_path.write_text(
+        "[Debug](https://docs.specfact.io/core-cli/debug-logging/)\n"
+        "[Debug anchor](https://docs.specfact.io/core-cli/debug-logging/#examining-ado-api-errors)\n"
+        "[Directory](https://docs.specfact.io/reference/directory-structure/)\n"
+        "[Feature keys](https://docs.specfact.io/reference/feature-keys/)\n",
+        encoding="utf-8",
+    )
+
+    findings = _script_attr(script, "_validate_core_docs_links")({doc_path: doc_path.read_text(encoding="utf-8")})
+
+    assert not findings
+
+
 def test_docs_review_workflow_runs_docs_command_validation() -> None:
     workflow = (REPO_ROOT / ".github" / "workflows" / "docs-review.yml").read_text(encoding="utf-8")