fix(update): preserve surviving hyperedges on AST-only rebuild (#1755)

`graphify update` (the watch._rebuild_code / _reconcile_existing_graph path)
evicted every hyperedge whose source_file is in the corpus, because on a full
update every corpus file counts as "rebuilt" and hyperedge eviction reused the
node/edge eviction set. But the AST pass never emits hyperedges, so nothing
replaced them — doc-sourced hyperedges (what semantic extraction produces) were
permanently lost on the first update after a full build, even on a no-op run.

Split out a hyperedge_evicted_source_identities set scoped to genuinely deleted
(and symlink-target-outside) sources only, not merely-rebuilt ones. Replacement-
by-id (new_hyperedge_ids) and dangling-member cleanup are unchanged, so a real
semantic re-extraction still replaces its own hyperedges and orphaned ones are
still dropped. Parametrized regression test (full + incremental doc update).

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

CHANGELOG.md

@@ -4,6 +4,8 @@ Full release notes with details on each version: [GitHub Releases](https://githu
 
 ## 0.9.12 (unreleased)
 
+- Fix: `graphify update` no longer deletes semantic hyperedges on every run (#1755, thanks @oleksii-tumanov). The AST-only rebuild treated every rebuilt corpus file as grounds to evict hyperedges anchored to it, but the AST pass never re-emits hyperedges, so doc-sourced hyperedges (exactly what semantic extraction produces) were permanently lost on the first `update` after a full build — even a no-op run. Hyperedge eviction is now scoped to genuinely deleted (or symlink-outside) sources, mirroring node/edge handling; replacement-by-id and dangling-member cleanup are unchanged.
+
 - Fix: Java member calls resolve against the receiver's declared type instead of a bare method-name match (#1696/#1697, thanks @oleksii-tumanov). `gw.charge()` where `gw: PaymentGateway` now binds to `PaymentGateway.charge`, not a same-named `AuditLog.charge` in another file. Explicit-type receivers and `this` are exact; current-class fields, method parameters, and explicitly-typed locals resolve via a method-scoped type table; a missing, ambiguous, inherited, or chained receiver is skipped rather than guessed (same god-node guard as the C#/Swift/Ruby resolvers). Fully-qualified and nested-type receivers are deferred (they need package/nesting-aware type identity).
 
 - Fix: output/cache artifacts no longer land in the scanned corpus or CWD when `--out`/`--graph` point elsewhere (#1747, thanks @bbqboogiedwonsen). `extract <corpus> --out <dir>` correctly wrote the graph to `<dir>` but `detect()`'s word-count/stat-index cache still created a stray `graphify-out/cache/` inside the corpus (it uses the scan root); it now honors the `--out` dir via a threaded `cache_root`. And `cluster-only --graph <elsewhere>/graphify-out/graph.json` wrote `GRAPH_REPORT.md`/labels/analysis/re-clustered graph to the CWD instead of beside the input; it now writes beside `--graph` when that graph lives in a `graphify-out/` dir, while still restoring into the CWD for an archived `backup/graph.json` (#934).

graphify/watch.py

@@ -407,6 +407,7 @@ def _reconcile_existing_graph(
             source_paths.absolute_identity(str(path), project_root) for path in extract_targets
         }
         node_evicted_source_identities = set(deleted_source_identities)
+        hyperedge_evicted_source_identities = set(deleted_source_identities)
         if not full_rebuild:
             node_evicted_source_identities.update(rebuilt_source_identities)
         edge_evicted_source_identities = (
@@ -431,6 +432,7 @@ def _reconcile_existing_graph(
                 if identity:
                     node_evicted_source_identities.add(identity)
                     edge_evicted_source_identities.add(identity)
+                    hyperedge_evicted_source_identities.add(identity)
 
         # A full re-extraction owns every AST node under watch_root. Incremental
         # extraction owns only nodes from rebuilt or deleted sources. Semantic
@@ -473,7 +475,7 @@ def _reconcile_existing_graph(
         for edge in existing.get("hyperedges", []):
             members = edge.get("nodes", edge.get("members", edge.get("node_ids", [])))
             if edge.get("id") in new_hyperedge_ids or source_paths.is_evicted(
-                edge, edge_evicted_source_identities
+                edge, hyperedge_evicted_source_identities
             ):
                 continue
             if isinstance(members, list) and any(member not in all_ids for member in members):

tests/test_watch.py

@@ -276,6 +276,57 @@ def _add_unrelated_semantic_pair(graph_path):
     graph_path.write_text(json.dumps(data), encoding="utf-8")
 
 
+@pytest.mark.parametrize(
+    "changed_paths",
+    [None, [Path("doc.md")]],
+    ids=["full-update", "incremental-doc-update"],
+)
+def test_rebuild_code_preserves_hyperedges_for_rebuilt_surviving_source(
+    tmp_path, changed_paths
+):
+    """#1755: AST-only updates must not drop semantic hyperedges whose members survive."""
+    from graphify.watch import _rebuild_code
+
+    corpus = tmp_path / "corpus"
+    corpus.mkdir()
+    (corpus / "doc.md").write_text(
+        "# Design\n\n## Flow\n\nDetails.\n", encoding="utf-8"
+    )
+
+    assert _rebuild_code(corpus, no_cluster=True, acquire_lock=False) is True
+    graph_path = corpus / "graphify-out" / "graph.json"
+    data = json.loads(graph_path.read_text(encoding="utf-8"))
+    assert {"doc", "doc_design"} <= {node["id"] for node in data["nodes"]}
+    data["hyperedges"] = [{
+        "id": "doc_flow_group",
+        "label": "Doc flow group",
+        "nodes": ["doc", "doc_design"],
+        "relation": "implements",
+        "confidence": "EXTRACTED",
+        "confidence_score": 1.0,
+        "source_file": "doc.md",
+    }]
+    graph_path.write_text(json.dumps(data), encoding="utf-8")
+
+    assert _rebuild_code(
+        corpus,
+        changed_paths=changed_paths,
+        no_cluster=True,
+        acquire_lock=False,
+    ) is True
+
+    after = json.loads(graph_path.read_text(encoding="utf-8"))
+    assert after["hyperedges"] == [{
+        "id": "doc_flow_group",
+        "label": "Doc flow group",
+        "nodes": ["doc", "doc_design"],
+        "relation": "implements",
+        "confidence": "EXTRACTED",
+        "confidence_score": 1.0,
+        "source_file": "doc.md",
+    }]
+
+
 @pytest.mark.parametrize(
     "changed_paths",
     [None, [Path("only.py")]],