Clean stale symbol references (#1785)

Author: Widthdom

changelog.d/unreleased/1785.fixed.md

@@ -0,0 +1,16 @@
+---
+category: fixed
+issues:
+  - 1785
+affected:
+  - src/CodeIndex/Database/DbWriter.cs
+  - tests/CodeIndex.Tests/DatabaseTests.cs
+---
+
+## English
+
+- **Stale file purges remove cross-file references to symbols defined only by the purged files (#1785)** — cleanup now drops phantom symbol edges when a deleted file was the only remaining definition for the referenced name.
+
+## 日本語
+
+- **stale file purge が purge 対象ファイルにしか定義が残っていないシンボルへの cross-file reference を削除するようになりました (#1785)** — 削除済みファイルが参照名の唯一の定義だった場合、phantom symbol edge を cleanup で取り除きます。

src/CodeIndex/Database/DbWriter.cs

@@ -578,6 +578,8 @@ private void DeleteFilesByIdBatched(IEnumerable<long> fileIds, int batchSize = D
 
     private void DeleteFileIdBatch(IReadOnlyList<long> fileIds)
     {
+        DeleteCrossFileReferencesToSymbolsDefinedOnlyByFiles(fileIds);
+
         using var deleteCmd = _conn.CreateCommand();
         var parameters = new List<string>(fileIds.Count);
         for (var i = 0; i < fileIds.Count; i++)
@@ -591,6 +593,38 @@ private void DeleteFileIdBatch(IReadOnlyList<long> fileIds)
         deleteCmd.ExecuteNonQuery();
     }
 
+    private void DeleteCrossFileReferencesToSymbolsDefinedOnlyByFiles(IReadOnlyList<long> fileIds)
+    {
+        using var deleteCmd = _conn.CreateCommand();
+        var parameters = new List<string>(fileIds.Count);
+        for (var i = 0; i < fileIds.Count; i++)
+        {
+            var parameterName = $"@id{i}";
+            parameters.Add(parameterName);
+            deleteCmd.Parameters.Add(parameterName, SqliteType.Integer).Value = fileIds[i];
+        }
+
+        var idList = string.Join(", ", parameters);
+        deleteCmd.CommandText = $@"
+            DELETE FROM symbol_references
+            WHERE file_id NOT IN ({idList})
+              AND symbol_name IS NOT NULL
+              AND symbol_name <> ''
+              AND EXISTS (
+                  SELECT 1
+                  FROM symbols deleted_symbols
+                  WHERE deleted_symbols.file_id IN ({idList})
+                    AND deleted_symbols.name = symbol_references.symbol_name
+              )
+              AND NOT EXISTS (
+                  SELECT 1
+                  FROM symbols retained_symbols
+                  WHERE retained_symbols.file_id NOT IN ({idList})
+                    AND retained_symbols.name = symbol_references.symbol_name
+              )";
+        deleteCmd.ExecuteNonQuery();
+    }
+
     private static string GetRelativeDirectory(string relativePath)
     {
         var normalized = relativePath.Replace('\\', '/');

tests/CodeIndex.Tests/DatabaseTests.cs

@@ -138,6 +138,52 @@ INSERT INTO symbol_references (
         Assert.Equal(0L, reader.GetInt64(1));
     }
 
+    [Fact]
+    public void PurgeStaleFiles_RemovesCrossFileReferencesToSymbolsDefinedOnlyByDeletedFiles()
+    {
+        var projectRoot = TestProjectHelper.CreateTempProject("purge-stale-symbol-ref");
+        try
+        {
+            Directory.CreateDirectory(Path.Combine(projectRoot, "src"));
+            File.WriteAllText(Path.Combine(projectRoot, "src", "target.py"), "# retained rename target");
+
+            var callerFileId = UpsertTestFile("src/caller.cs", checksum: "caller");
+            var staleTargetFileId = UpsertTestFile("src/target.cs", checksum: "target");
+            _ = UpsertTestFile("src/target.py", checksum: "target");
+            _writer.InsertSymbols([
+                new SymbolRecord
+                {
+                    FileId = staleTargetFileId,
+                    Kind = "function",
+                    Name = "DeletedTarget",
+                    Line = 1,
+                },
+            ]);
+            _writer.InsertReferences([
+                new ReferenceRecord
+                {
+                    FileId = callerFileId,
+                    SymbolName = "DeletedTarget",
+                    ReferenceKind = "call",
+                    Line = 1,
+                    Column = 1,
+                    Context = "DeletedTarget();",
+                },
+            ]);
+
+            var purged = _writer.PurgeStaleFilesSharingDirectoryAndStem(projectRoot, "src/target.py");
+
+            Assert.Equal(1, purged);
+            using var cmd = _db.Connection.CreateCommand();
+            cmd.CommandText = "SELECT COUNT(*) FROM symbol_references WHERE symbol_name = 'DeletedTarget'";
+            Assert.Equal(0L, (long)cmd.ExecuteScalar()!);
+        }
+        finally
+        {
+            TestProjectHelper.DeleteDirectory(projectRoot);
+        }
+    }
+
     [Fact]
     public void OptimizeFts_ResetsIncrementalWriteCounterAndStampsTime()
     {