fix(provenance): reset in-memory chain state on clear

semantica/provenance/storage.py

@@ -317,6 +317,9 @@ class InMemoryStorage(ProvenanceStorage):
         """
         count = len(self._entries)
         self._entries.clear()
+        with self._seq_lock:
+            self._seq_counter = 0
+            self._chain_head = None
         return count
 
     @contextmanager

tests/provenance/test_manager.py

@@ -466,6 +466,30 @@ class TestProvenanceManager:
         lineage = prov_mgr.get_lineage("entity_1")
         assert lineage == {}
 
+    def test_clear_resets_chain_state(self):
+        """Regression: clear() must fully reset chain state so the first write
+        after clear starts a fresh chain and verify_chain() passes."""
+        prov_mgr = ProvenanceManager()
+
+        prov_mgr.track_entity("e1", source="doc1")
+        prov_mgr.track_entity("e2", source="doc1")
+        prov_mgr.clear()
+
+        # Chain head must be empty immediately after clear
+        assert prov_mgr.storage.get_chain_head() is None
+
+        # First write after clear starts a fresh chain (sequence_id=1, previous_checksum=None)
+        entry = prov_mgr.track_entity("e3", source="doc2")
+        assert entry.sequence_id == 1
+        assert entry.previous_checksum is None
+
+        # verify_chain() must pass on the fresh chain
+        prov_mgr.track_entity("e4", source="doc2")
+        result = prov_mgr.verify_chain()
+        assert result["valid"] is True
+        assert result["total_entries"] == 2
+        assert result["broken_links"] == []
+
     def test_retrack_with_explicit_parent_overrides_history_link(self):
         """#742 — re-tracking an entity with an explicit parent_entity_id must
         honor the new value, not silently replace it with an auto-generated

tests/provenance/test_storage.py

@@ -135,6 +135,31 @@ class TestInMemoryStorage:
         assert count == 1
         assert len(storage.retrieve_all()) == 0
 
+    def test_clear_resets_chain_state(self):
+        """Issue #825 fix: clear() must reset chain state so get_chain_head()
+        returns None and the first write after clear starts a fresh chain."""
+        storage = InMemoryStorage()
+
+        entry1 = ProvenanceEntry(
+            entity_id="e1", entity_type="entity", activity_id="act",
+            sequence_id=1, checksum="checksum_1",
+        )
+        storage.store(entry1)
+        assert storage.get_chain_head() == (1, "checksum_1")
+
+        storage.clear()
+
+        # Chain head must be None after clear
+        assert storage.get_chain_head() is None
+
+        # First write after clear starts a fresh chain
+        entry2 = ProvenanceEntry(
+            entity_id="e2", entity_type="entity", activity_id="act",
+            sequence_id=1, checksum="checksum_fresh",
+        )
+        storage.store(entry2)
+        assert storage.get_chain_head() == (1, "checksum_fresh")
+
     def test_get_chain_head(self):
         """Issue #825, Part A item 2 — chain head reporting."""
         storage = InMemoryStorage()