fix(index): clear the legacy embeddings table on reset and deindex

CHANGELOG.md

@@ -64,6 +64,14 @@ All notable changes to vouch are documented here. Format follows
   per-prompt block, the session banner, `vouch status` and the opt-in
   question all say so rather than calling it "this repo's" knowledge.
 
+### Fixed
+- `vouch index` and artifact deletion now clear the legacy `embeddings`
+  vector table. `index_db.reset()` promised to drop every derived table
+  but skipped it, and `deindex()` only cleared `embedding_index` — so a
+  deleted artifact's vector kept returning as a semantic-search hit, and
+  fsck's `orphan_embedding` warning was permanent: the natural remedy
+  (reindexing) could never clear it.
+
 ## [1.5.0] — 2026-07-20
 
 ### Added

src/vouch/index_db.py

@@ -122,6 +122,7 @@ def reset(kb_dir: Path) -> None:
             "DELETE FROM claims_fts;"
             "DELETE FROM pages_fts;"
             "DELETE FROM entities_fts;"
+            "DELETE FROM embeddings;"
             "DELETE FROM embedding_index;"
             "DELETE FROM query_embedding_cache;"
             "DELETE FROM embedding_dupes;"
@@ -190,18 +191,22 @@ def deindex(conn: sqlite3.Connection, *, kind: str, id: str) -> None:
     """Remove every derived index row for a deleted artifact.
 
     FTS row for claim/page/entity (relations have no FTS table); the
-    embedding row for any kind (every put_* calls _embed_and_store, so an
-    embedding may exist for a relation too); and any provenance edge that
-    touches the id. prov_edges is otherwise rebuildable via
-    `kb.provenance_rebuild` — this keeps state.db consistent without a
-    full rebuild.
+    embedding rows for any kind — both the legacy `embeddings` vector
+    table that `search_embeddings` scans and the newer `embedding_index`
+    (every put_* calls _embed_and_store, so an embedding may exist for a
+    relation too); and any provenance edge that touches the id.
+    prov_edges is otherwise rebuildable via `kb.provenance_rebuild` —
+    this keeps state.db consistent without a full rebuild.
     """
     if kind == "claim":
         conn.execute("DELETE FROM claims_fts WHERE id = ?", (id,))
     elif kind == "page":
         conn.execute("DELETE FROM pages_fts WHERE id = ?", (id,))
     elif kind == "entity":
         conn.execute("DELETE FROM entities_fts WHERE id = ?", (id,))
+    conn.execute(
+        "DELETE FROM embeddings WHERE kind = ? AND id = ?", (kind, id)
+    )
     conn.execute(
         "DELETE FROM embedding_index WHERE kind = ? AND id = ?", (kind, id)
     )

tests/test_health.py

@@ -356,6 +356,25 @@ def test_fsck_orphan_embedding(store: KBStore) -> None:
     assert "orphan_embedding" in codes
 
 
+def test_fsck_orphan_embedding_cleared_by_reindex(store: KBStore) -> None:
+    """A reindex is the natural remedy for an orphan embedding, but
+    reset() skipped the legacy `embeddings` table, so the ghost vector
+    survived `vouch index` and the fsck warning could never be cleared."""
+    src = store.put_source(b"e")
+    c = Claim(id="real", text="t", evidence=[src.id])
+    store.put_claim(c)
+    with index_db.open_db(store.kb_dir) as conn:
+        index_db.index_embedding(conn, kind="claim", id="ghost", vec=[0.1, 0.2])
+    assert "orphan_embedding" in {f.code for f in health.fsck(store).findings}
+
+    health.rebuild_index(store)
+
+    report = health.fsck(store)
+    assert "orphan_embedding" not in {f.code for f in report.findings}, (
+        "reindex did not clear the orphaned legacy embedding row"
+    )
+
+
 def test_fsck_surfaces_invalid_claim_yaml_without_crashing(
     store: KBStore,
 ) -> None:

tests/test_index.py

@@ -47,3 +47,30 @@ def test_index_via_approve(store: KBStore) -> None:
     approve(store, pr.id, approved_by="u")
     hits = index_db.search(store.kb_dir, "indexed")
     assert any(k == "claim" for k, *_ in hits)
+
+
+def test_reset_clears_legacy_embeddings_table(store: KBStore) -> None:
+    """reset() promises to clear every derived table, embedding vectors
+    included — but the legacy `embeddings` table (the one
+    `search_embeddings` scans) was left out, so a deleted artifact's
+    vector survived a full reindex and kept coming back as a semantic
+    hit: exactly the orphaned-hits case the docstring warns about."""
+    with index_db.open_db(store.kb_dir) as conn:
+        index_db.index_embedding(conn, kind="claim", id="ghost", vec=[0.1, 0.2])
+
+    index_db.reset(store.kb_dir)
+
+    with index_db.open_db(store.kb_dir) as conn:
+        count = conn.execute("SELECT COUNT(*) FROM embeddings").fetchone()[0]
+    assert count == 0
+
+
+def test_deindex_removes_legacy_embedding_row(store: KBStore) -> None:
+    """deindex() documents removing the embedding rows for a deleted
+    artifact; it cleared `embedding_index` but left the legacy
+    `embeddings` row behind."""
+    with index_db.open_db(store.kb_dir) as conn:
+        index_db.index_embedding(conn, kind="claim", id="c1", vec=[0.1, 0.2])
+        index_db.deindex(conn, kind="claim", id="c1")
+        count = conn.execute("SELECT COUNT(*) FROM embeddings").fetchone()[0]
+    assert count == 0