fix: _apply_links overwrites related_skills regardless of current value

tests/test_link.py

@@ -243,6 +243,19 @@ def test_duplicate_targets_deduplicated(self):
         )
         self.assertEqual(fm_line.count("invoice-compare"), 1)
 
+    def test_existing_real_value_overwritten(self):
+        """Regression: a second link-ingest run must overwrite an existing real
+        related_skills value, not leave it stale. Previously only placeholder
+        sentinels (none / PLACEHOLDER / [PLACEHOLDER]) were matched, so this
+        silently skipped the frontmatter update while still rewriting the body
+        table — leaving frontmatter and body inconsistent."""
+        text = _make_skill("file-delivery", related_skills_value="invoice-compare")
+        links = [{"to": "payment-method", "type": "calls", "reason": "needs payment"}]
+        result = _apply_links(text, links)
+        fm_line = next(l for l in result.splitlines() if l.startswith("related_skills:"))
+        self.assertEqual(fm_line, "related_skills: payment-method",
+                         "existing related_skills value must be replaced, not left stale")
+
 
 class TestApplyLinksRelatedSkillsTable(unittest.TestCase):
     def test_table_row_inserted(self):

tools/skill_generator/link.py

@@ -118,13 +118,19 @@ def _apply_links(text: str, links: list) -> str:
     """Update frontmatter `related_skills:` and the body Related Skills table."""
     targets = [ln["to"] for ln in links]
     joined = ", ".join(sorted(set(targets)))
-    text = re.sub(
-        r"^related_skills:\s*(?:PLACEHOLDER|none|\[PLACEHOLDER\])\s*$",
-        f"related_skills: {joined}",
-        text,
-        count=1,
-        flags=re.MULTILINE,
-    )
+    # Update the frontmatter field for any existing value — not just placeholder
+    # sentinels.  Prior to this fix, a second link-ingest run (e.g., after a
+    # Phase 2 update) left the frontmatter stale while rewriting the body table,
+    # creating a schema inconsistency.  Guard against empty joined so a caller
+    # with no links doesn't blank out an existing value.
+    if joined:
+        text = re.sub(
+            r"^related_skills:\s*.*$",
+            f"related_skills: {joined}",
+            text,
+            count=1,
+            flags=re.MULTILINE,
+        )
     table_rows = "\n".join(
         f"| {ln['to']} | {ln.get('type', 'calls')} | {ln.get('reason', '')} |"
         for ln in links