fix(build_merge): replace re-extracted files instead of accumulating stale edges (#1344)

build_merge: prune a re-extracted file's stale nodes/edges before merge instead of accumulating (fixes #1283, #1285). Validated: full suite 2107 passed. Thanks @RelywOo.

graphify/build.py

@@ -443,8 +443,11 @@ def build_merge(
 ) -> nx.Graph:
     """Load existing graph.json, merge new chunks into it, and save back.
 
-    Never replaces - only grows (or prunes deleted-file nodes via prune_sources).
-    Safe to call repeatedly: existing nodes and edges are preserved.
+    Re-extracted files REPLACE their prior contribution: any source_file present
+    in new_chunks is dropped from the loaded graph before merging, so a changed
+    file's stale nodes/edges don't accumulate. Files absent from new_chunks are
+    preserved unchanged; deleted files are removed via prune_sources.
+    Safe to call repeatedly.
     root: if given, absolute source_file paths in new_chunks are made relative (#932).
     """
     graph_path = Path(graph_path)
@@ -462,10 +465,40 @@ def build_merge(
         links_key = "links" if "links" in data else "edges"
         existing_nodes = list(data.get("nodes", []))
         existing_edges = list(data.get(links_key, []))
-        base = [{"nodes": existing_nodes, "edges": existing_edges}]
+        had_graph = True
     else:
         existing_nodes = []
-        base = []
+        existing_edges = []
+        had_graph = False
+
+    # Re-extracted files REPLACE their prior contribution. Every source_file
+    # present in new_chunks is dropped from the loaded base before merging, so a
+    # CHANGED file's stale nodes/edges don't accumulate across incremental
+    # updates. Without this, build() merges old+new for the same file and only
+    # exact-duplicate edges collapse — edges/nodes that disappeared from the new
+    # version survive forever. Brand-new files aren't in base, so this is a no-op
+    # for them; genuinely deleted files are still handled via prune_sources.
+    # Matched in both raw and _norm_source_file form because new_chunks may carry
+    # absolute win32 paths while the stored graph keeps relative posix (#1007).
+    _replace_root = str(Path(root).resolve()) if root is not None else None
+    new_sources: set[str] = set()
+    for ch in new_chunks:
+        for n in ch.get("nodes", []):
+            sf = n.get("source_file")
+            if not sf:
+                continue
+            new_sources.add(sf)
+            norm = _norm_source_file(sf, _replace_root)
+            if norm:
+                new_sources.add(norm)
+    if new_sources:
+        def _kept(item: dict) -> bool:
+            sf = item.get("source_file")
+            return sf not in new_sources and _norm_source_file(sf, _replace_root) not in new_sources
+        existing_nodes = [n for n in existing_nodes if _kept(n)]
+        existing_edges = [e for e in existing_edges if _kept(e)]
+
+    base = [{"nodes": existing_nodes, "edges": existing_edges}] if had_graph else []
 
     all_chunks = base + list(new_chunks)
     G = build(all_chunks, directed=directed, dedup=dedup, dedup_llm_backend=dedup_llm_backend, root=root)