Fix code review findings: metadata precedence and Mapping support

- get_lineage() aggregated metadata by iterating trace_lineage()'s BFS
  order and calling dict.update() on each entry, so ancestor metadata
  (now reachable via derived_from chains) could overwrite the queried
  entity's own metadata on conflicting keys. Reverse the iteration so
  the queried entity (always lineage_entries[0]) is applied last and
  wins, matching the documented "most recent entry's metadata takes
  precedence" intent.
- track_entity()'s derived_from guard only accepted a concrete dict,
  silently ignoring other collections.abc.Mapping implementations
  (e.g. types.MappingProxyType). Switch the isinstance check to
  Mapping so any mapping-like metadata is honored.

Addresses Qodo review findings on PR #741.

CHANGELOG.md

@@ -26,7 +26,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
   - `track_entity()`'s only auto-linking logic looked up `source` as if it were an existing entity's `entity_id`, so passing the same real URL/DOI as `source` for two conceptually linked entities (e.g. a document and a decision derived from it) never produced a parent link, leaving `get_lineage()` returning a chain of length 1
   - `metadata["derived_from"]` was preserved and echoed back in the output JSON but was never consulted by any linking or traversal code, so the caller's explicit relationship was silently inert
   - `track_entity()` now treats `metadata["derived_from"]` as an explicit parent link (unless `parent_entity_id` was already passed directly), so `InMemoryStorage.trace_lineage()`'s existing BFS over `parent_entity_id` picks it up for free
-  - Added 7 regression/edge-case tests in `tests/provenance/test_manager.py` covering the happy path, explicit `parent_entity_id` precedence over `derived_from`, precedence over the `source`-as-known-entity-id fallback, a `derived_from` pointing at a never-tracked entity, non-string/empty-string `derived_from` values being ignored, a self-referencing `derived_from` not hanging traversal, and multi-hop `derived_from` chains, closing #735
+  - `metadata["derived_from"]` is now recognized on any `collections.abc.Mapping`, not just a concrete `dict`, so e.g. `types.MappingProxyType` metadata still creates the parent link
+  - `get_lineage()`'s metadata aggregation now applies the queried entity's own metadata last so it wins over ancestor metadata on conflicting keys, matching the documented "most recent entry's metadata takes precedence" behavior — previously `trace_lineage()`'s BFS order caused ancestor metadata (now reachable via `derived_from` chains) to silently overwrite the queried entity's own values
+  - Added 9 regression/edge-case tests in `tests/provenance/test_manager.py` covering the happy path, explicit `parent_entity_id` precedence over `derived_from`, precedence over the `source`-as-known-entity-id fallback, a `derived_from` pointing at a never-tracked entity, non-string/empty-string `derived_from` values being ignored, a self-referencing `derived_from` not hanging traversal, multi-hop `derived_from` chains, metadata precedence between a queried entity and its ancestors, and non-`dict` `Mapping` metadata, closing #735
 
 - **`InferenceResult.premises` always empty from `forward_chain`/`backward_chain`** (#739) by @Sameer6305
   - `_match_rule()` discarded matched facts and returned only instantiated conclusions, so `ExplanationGenerator` always produced empty premises lists regardless of which facts actually satisfied a rule, closing #733

semantica/provenance/manager.py

@@ -25,6 +25,7 @@ License: MIT
 """
 
 from typing import Optional, List, Dict, Any
+from collections.abc import Mapping
 from datetime import datetime
 
 from .schemas import ProvenanceEntry, SourceReference, PropertySource
@@ -118,7 +119,7 @@ class ProvenanceManager:
 
         # If caller declared an explicit parent via metadata, honor it
         # (unless parent_entity_id was already passed directly)
-        if not parent_id and metadata and isinstance(metadata, dict):
+        if not parent_id and metadata and isinstance(metadata, Mapping):
             derived_from = metadata.get("derived_from")
             if derived_from and isinstance(derived_from, str):
                 parent_id = derived_from
@@ -460,10 +461,14 @@ class ProvenanceManager:
         if not lineage_entries:
             return {}
         
-        # Aggregate metadata from all lineage entries
-        # Most recent entry's metadata takes precedence
+        # Aggregate metadata from all lineage entries.
+        # trace_lineage() is a BFS starting at entity_id, so lineage_entries[0]
+        # is always the queried entity itself, followed by its ancestors
+        # (parent, grandparent, ...). Apply ancestors first and the queried
+        # entity last so its own keys win on conflict, matching the intent
+        # that the "most recent"/current entity's metadata takes precedence.
         aggregated_metadata = {}
-        for entry in lineage_entries:
+        for entry in reversed(lineage_entries):
             if entry.metadata:
                 meta = entry.metadata
                 if isinstance(meta, str):

tests/provenance/test_manager.py

@@ -248,6 +248,48 @@ class TestProvenanceManager:
 
         assert entry.parent_entity_id is None
 
+    def test_get_lineage_metadata_prefers_queried_entity_over_ancestors(self):
+        """Aggregated lineage metadata should let the queried entity's own
+        values win over ancestor values on conflicting keys, matching the
+        documented "most recent entry's metadata takes precedence" intent."""
+        prov_mgr = ProvenanceManager()
+
+        prov_mgr.track_entity(
+            entity_id="ancestor",
+            source="doc_1",
+            metadata={"status": "draft", "shared_only_on_ancestor": True},
+        )
+        prov_mgr.track_entity(
+            entity_id="descendant",
+            source="doc_1",
+            metadata={"status": "final", "derived_from": "ancestor"},
+        )
+
+        lineage = prov_mgr.get_lineage("descendant")
+
+        assert lineage["metadata"]["status"] == "final"
+        assert lineage["metadata"]["shared_only_on_ancestor"] is True
+
+    def test_derived_from_accepts_non_dict_mapping(self):
+        """metadata['derived_from'] should be honored for any Mapping
+        implementation, not just a concrete dict (e.g. types.MappingProxyType
+        or a custom collections.abc.Mapping)."""
+        from types import MappingProxyType
+
+        prov_mgr = ProvenanceManager()
+
+        prov_mgr.track_entity(entity_id="mapping_parent", source="doc_1")
+        entry = prov_mgr.track_entity(
+            entity_id="mapping_child",
+            source="doc_1",
+            metadata=MappingProxyType({"derived_from": "mapping_parent"}),
+        )
+
+        assert entry.parent_entity_id == "mapping_parent"
+
+        lineage = prov_mgr.get_lineage("mapping_child")
+        assert lineage["entity_count"] == 2
+
     def test_batch_entity_tracking(self):
         """Test batch entity tracking."""
         prov_mgr = ProvenanceManager()