Fix MCP reader cleanup and error reporting

changelog.d/unreleased/1714.fixed.md

@@ -0,0 +1,17 @@
+---
+category: fixed
+issues:
+  - 1714
+affected:
+  - src/CodeIndex/Database/DbReader.cs
+  - src/CodeIndex/Mcp/McpServer.cs
+  - src/CodeIndex/Mcp/McpToolHandlers.cs
+---
+
+## English
+
+- **MCP DbReader lifetimes are now disposed deterministically (#1714)** - per-request readers and the index-project signal reader release their per-reader caches when the call finishes.
+
+## 日本語
+
+- **MCP の DbReader lifetime を決定的に破棄するようにしました (#1714)** - リクエスト単位の reader と index-project の signal reader が、呼び出し終了時に reader 内キャッシュを解放します。

changelog.d/unreleased/1716.fixed.md

@@ -0,0 +1,15 @@
+---
+category: fixed
+issues:
+  - 1716
+affected:
+  - src/CodeIndex/Cli/ProgramRunner.cs
+---
+
+## English
+
+- **MCP server startup now handles loop failures before process exit (#1716)** - stdio and HTTP MCP entry points log unexpected failures and flush stdout/stderr before returning an error exit code.
+
+## 日本語
+
+- **MCP server 起動経路がループ失敗をプロセス終了前に処理するようにしました (#1716)** - stdio / HTTP MCP の entry point は予期しない失敗をログに残し、stdout/stderr を flush してからエラー終了します。

changelog.d/unreleased/1720.fixed.md

@@ -0,0 +1,15 @@
+---
+category: fixed
+issues:
+  - 1720
+affected:
+  - src/CodeIndex/Mcp/McpToolHandlers.cs
+---
+
+## English
+
+- **MCP index now reports per-file failures instead of silently swallowing them (#1720)** - index responses include `failed_count` and a capped failure list when individual files fail.
+
+## 日本語
+
+- **MCP index がファイル単位の失敗を黙殺せず報告するようにしました (#1720)** - 個別ファイルの処理に失敗した場合、応答に `failed_count` と上限付きの失敗一覧を含めます。

changelog.d/unreleased/2010.fixed.md

@@ -0,0 +1,15 @@
+---
+category: fixed
+issues:
+  - 2010
+affected:
+  - src/CodeIndex/Database/DbDebug.cs
+---
+
+## English
+
+- **DbDebug now preserves row-read exception chains (#2010)** - debug dumps include exception chains captured while snapshotting row fields and a root-cause line for faster diagnosis.
+
+## 日本語
+
+- **DbDebug が row read 例外チェーンを保持するようにしました (#2010)** - 行フィールドの snapshot 中に捕捉した例外チェーンと root-cause 行を debug dump に含め、原因特定を容易にします。

src/CodeIndex/Cli/ProgramRunner.cs

@@ -1451,8 +1451,25 @@ private static int RunMcp(string[] cmdArgs, string appVersion)
             if (string.Equals(transport, "http", StringComparison.OrdinalIgnoreCase))
                 return RunMcpHttp(server, listenSpec ?? DefaultMcpHttpListen);
 
-            server.RunAsync().GetAwaiter().GetResult();
-            return CommandExitCodes.Success;
+            try
+            {
+                server.RunAsync().GetAwaiter().GetResult();
+                return CommandExitCodes.Success;
+            }
+            catch (OperationCanceledException)
+            {
+                Console.Out.Flush();
+                Console.Error.Flush();
+                return CommandExitCodes.CancelledBySignal;
+            }
+            catch (Exception ex)
+            {
+                GlobalToolLog.Error("mcp_server_failed " + GlobalToolLog.FormatExceptionChain(ex));
+                Console.Error.WriteLine($"Error: MCP server failed ({ex.GetType().Name}: {ex.Message}).");
+                Console.Out.Flush();
+                Console.Error.Flush();
+                return CommandExitCodes.DatabaseError;
+            }
         }
         finally
         {
@@ -1516,7 +1533,24 @@ private static int RunMcpHttp(McpServer server, string listenSpec)
                 else
                     Console.Error.WriteLine($"[cdidx-mcp] HTTP transport listening on {resolved.Prefix} (bearer auth required).");
 
-                server.RunAsync(transport, cts.Token).GetAwaiter().GetResult();
+                try
+                {
+                    server.RunAsync(transport, cts.Token).GetAwaiter().GetResult();
+                }
+                catch (OperationCanceledException)
+                {
+                    Console.Out.Flush();
+                    Console.Error.Flush();
+                    return CommandExitCodes.CancelledBySignal;
+                }
+                catch (Exception ex)
+                {
+                    GlobalToolLog.Error("mcp_http_server_failed " + GlobalToolLog.FormatExceptionChain(ex));
+                    Console.Error.WriteLine($"Error: MCP HTTP server failed ({ex.GetType().Name}: {ex.Message}).");
+                    Console.Out.Flush();
+                    Console.Error.Flush();
+                    return CommandExitCodes.DatabaseError;
+                }
             }
         }
         finally

src/CodeIndex/Database/DbDebug.cs

@@ -40,6 +40,10 @@ public static class DbDebug
     [ThreadStatic]
     private static List<(string Name, string Value)>? _lastRow;
     [ThreadStatic]
+    private static List<string>? _lastRowReadExceptionChains;
+    [ThreadStatic]
+    private static List<Exception>? _lastRowReadExceptions;
+    [ThreadStatic]
     private static bool _hasContext;
     [ThreadStatic]
     private static List<QueryProfileEntry>? _profileEntries;
@@ -169,6 +173,8 @@ public static void ResetContext()
         _lastSql = null;
         _lastParams = null;
         _lastRow = null;
+        _lastRowReadExceptionChains = null;
+        _lastRowReadExceptions = null;
         _hasContext = false;
     }
 
@@ -314,6 +320,9 @@ internal static void SnapshotRow(SqliteDataReader reader)
             catch (Exception ex)
             {
                 row.Add((name, $"<error: {ex.GetType().Name}: {ex.Message}>"));
+                (_lastRowReadExceptions ??= new List<Exception>()).Add(ex);
+                (_lastRowReadExceptionChains ??= new List<string>())
+                    .Add($"[{name}]\n{GlobalToolLog.FormatExceptionChain(ex, includeStacks: mode == DebugMode.Unsafe)}");
             }
         }
         _lastRow = row;
@@ -356,6 +365,15 @@ public static void DumpToStderr(Exception ex)
             foreach (var (name, value) in _lastRow)
                 sb.AppendLine($"  [{name}] = {value}");
         }
+        if (_lastRowReadExceptionChains is { Count: > 0 })
+        {
+            sb.AppendLine("Row read exception chains:");
+            foreach (var chain in _lastRowReadExceptionChains)
+                sb.AppendLine(chain);
+        }
+        var rootCause = GetDeepestExceptionIncludingRowReads(ex);
+        if (_lastRowReadExceptionChains is { Count: > 0 })
+            sb.AppendLine($"Root cause: {rootCause.GetType().Name}: {rootCause.Message}");
         if (mode != DebugMode.Unsafe && ex.StackTrace != null)
         {
             sb.AppendLine("Stack:");
@@ -365,6 +383,25 @@ public static void DumpToStderr(Exception ex)
         Console.Error.Write(sb.ToString());
     }
 
+    private static Exception GetDeepestException(Exception ex)
+    {
+        var current = ex;
+        while (current.InnerException != null)
+            current = current.InnerException;
+        return current;
+    }
+
+    private static Exception GetDeepestExceptionIncludingRowReads(Exception ex)
+    {
+        var deepest = GetDeepestException(ex);
+        if (_lastRowReadExceptions is not { Count: > 0 })
+            return deepest;
+
+        foreach (var rowException in _lastRowReadExceptions)
+            deepest = GetDeepestException(rowException);
+        return deepest;
+    }
+
     private static string FormatValue(object? value, DebugMode mode, string? valueName = null)
     {
         if (value is null || value is DBNull)

src/CodeIndex/Database/DbReader.cs

@@ -28,7 +28,7 @@ public readonly record struct SqlGraphContractSignal(
 /// Handles read/query operations against the database for search, symbols, and files.
 /// 検索・シンボル・ファイル一覧などのDB読み取り操作を担当する。
 /// </summary>
-public partial class DbReader
+public partial class DbReader : IDisposable
 {
     public const string VerifyFoldReadyRowsEnvironmentVariable = "CDIDX_VERIFY_FOLD_READY_ROWS";
     internal const int MaxReferenceKindAggregateCharacters = 16 * 1024;
@@ -65,6 +65,7 @@ public partial class DbReader
     private readonly Dictionary<string, List<CSharpContainingTypeCandidate>> _csharpTypeContainingTypesByName = new(StringComparer.OrdinalIgnoreCase);
     private readonly Dictionary<string, HashSet<string>> _csharpInheritedContainingTypesByQualifiedName = new(StringComparer.Ordinal);
     private readonly Dictionary<string, CSharpContainingTypeScope?> _csharpContainingTypeScopeByQualifiedName = new(StringComparer.Ordinal);
+    private bool _disposed;
     private HashSet<string>? _csharpGlobalUsingStaticTargets;
     private HashSet<string>? _csharpGlobalUsingNamespaces;
     private Dictionary<string, CSharpUsingAliasScope>? _csharpGlobalUsingAliasesByName;
@@ -563,6 +564,30 @@ private DbReader(
         (_indexNewerThanReader, _indexNewerThanReaderReason) = DetectNewerThanReaderContracts(_conn, userVersion);
     }
 
+    public void Dispose()
+    {
+        if (_disposed)
+            return;
+
+        _disposed = true;
+        _csharpUsingStaticScopesByPath.Clear();
+        _csharpNamespaceScopesByPath.Clear();
+        _csharpContainingTypeScopesByPath.Clear();
+        _csharpUsingNamespaceScopesByPath.Clear();
+        _csharpUsingAliasScopesByPath.Clear();
+        _activeCSharpTypeNamespacesByPathLine.Clear();
+        _activeCSharpContainingTypeScopesByPathLine.Clear();
+        _activeCSharpUsingStaticTargetsByPathLine.Clear();
+        _csharpConstantPatternContainersByMemberName.Clear();
+        _csharpTypeNamespacesByName.Clear();
+        _csharpTypeContainingTypesByName.Clear();
+        _csharpInheritedContainingTypesByQualifiedName.Clear();
+        _csharpContainingTypeScopeByQualifiedName.Clear();
+        _csharpGlobalUsingStaticTargets = null;
+        _csharpGlobalUsingNamespaces = null;
+        _csharpGlobalUsingAliasesByName = null;
+    }
+
     /// <summary>
     /// Per-request CancellationToken plumbed in by the caller (e.g. the MCP server). Methods
     /// that loop over SQLite rows can check this between batches to bail out promptly on

src/CodeIndex/Mcp/McpServer.cs

@@ -2518,7 +2518,7 @@ private JsonNode WithDbReader(JsonNode? id, JsonNode? args, Func<DbReader, JsonN
         {
             using var isolatedDb = new DbContext(_dbPath);
             isolatedDb.TryMigrateForRead();
-            var isolatedReader = new DbReader(isolatedDb, requestToken);
+            using var isolatedReader = new DbReader(isolatedDb, requestToken);
             isolatedReader.IncludeGenerated = args?["includeGenerated"]?.GetValue<bool>() ?? false;
             return isolatedReader.RunWithGeneratedScope(() => action(isolatedReader));
         }
@@ -2539,7 +2539,7 @@ private JsonNode WithDbReader(JsonNode? id, JsonNode? args, Func<DbReader, JsonN
         // MCP ツール呼び出しごとの schema 再走査を排除し (issue #1565)、
         // per-request cancellation token を reader に渡して SQLite 作業が
         // shutdown / 切断を観測できるようにする (#1567)。
-        var reader = new DbReader(db, requestToken);
+        using var reader = new DbReader(db, requestToken);
         reader.IncludeGenerated = args?["includeGenerated"]?.GetValue<bool>() ?? false;
         return reader.RunWithGeneratedScope(() => action(reader));
     }

src/CodeIndex/Mcp/McpToolHandlers.cs

@@ -2899,6 +2899,7 @@ void WriteProjectRootOnce()
         if (purged > 0 && hadCSharpStaticInterfaceContractsBeforePurge)
             csharpWorkspace = csharpWorkspace with { HasStaticInterfaceContracts = true };
         int processed = 0, skipped = 0, errors = 0;
+        var failures = new List<IndexFileFailure>();
         var reusedHotspotFamilyLanguages = new HashSet<string>(StringComparer.Ordinal);
 
         foreach (var filePath in files)
@@ -2970,9 +2971,10 @@ void WriteProjectRootOnce()
                         txn.Commit();
                     }
                 }
-                catch
+                catch (Exception ex)
                 {
                     errors++;
+                    failures.Add(BuildIndexFileFailure(projectPath, filePath, ex, "delete_skipped_binary"));
                 }
             }
             catch (Exception ex) when (ex is FileNotFoundException or DirectoryNotFoundException)
@@ -2991,9 +2993,10 @@ void WriteProjectRootOnce()
                         txn.Commit();
                     }
                 }
-                catch
+                catch (Exception cleanupEx)
                 {
                     errors++;
+                    failures.Add(BuildIndexFileFailure(projectPath, filePath, cleanupEx, "delete_missing_file"));
                 }
             }
             catch (OperationCanceledException) when (requestToken.IsCancellationRequested)
@@ -3002,11 +3005,12 @@ void WriteProjectRootOnce()
                     writer.ClearBatchInProgress();
                 throw;
             }
-            catch
+            catch (Exception ex)
             {
                 if (fileBatchMarked)
                     writer.ClearBatchInProgress();
                 errors++;
+                failures.Add(BuildIndexFileFailure(projectPath, filePath, ex, "index_file"));
             }
             processed++;
             EmitProgressNotification(progressToken, processed, files.Count);
@@ -3160,7 +3164,8 @@ void WriteProjectRootOnce()
                 ["skipped"] = skipped,
                 ["purged"] = purged,
                 ["unknown_extension_file_count"] = scanResult.UnknownExtensionFiles.Count,
-                ["errors"] = errors
+                ["errors"] = errors,
+                ["failed_count"] = failures.Count
             },
             ["sql_graph_contract_ready"] = sqlGraphContractReadyAfter,
             ["csharp_symbol_name_ready"] = csharpSymbolNameReadyAfter,
@@ -3170,9 +3175,28 @@ void WriteProjectRootOnce()
             ["fold_ready"] = foldReadyAfter,
             ["fold_ready_reason"] = foldReadyReason
         };
+        if (failures.Count > 0)
+        {
+            var failureArray = new JsonArray();
+            foreach (var failure in failures.Take(50))
+            {
+                failureArray.Add(new JsonObject
+                {
+                    ["path"] = failure.Path,
+                    ["stage"] = failure.Stage,
+                    ["exception_type"] = failure.ExceptionType,
+                    ["message"] = failure.Message,
+                });
+            }
+            structured["failed_count"] = failures.Count;
+            structured["failures"] = failureArray;
+            if (failures.Count > 50)
+                structured["failures_truncated"] = failures.Count - 50;
+            GlobalToolLog.Error($"mcp_index_file_failures count={failures.Count} first_path='{failures[0].Path}' first_error='{failures[0].ExceptionType}: {failures[0].Message}'");
+        }
         if (!sqlGraphContractReadyAfter)
         {
-            var signalReader = new DbReader(writer.Connection);
+            using var signalReader = new DbReader(writer.Connection);
             AddSqlGraphContractSignal(structured, signalReader.GetSqlGraphContractSignal());
         }
         return CreateToolResult(id,
@@ -3188,6 +3212,14 @@ void WriteProjectRootOnce()
             structured);
     }
 
+    private static IndexFileFailure BuildIndexFileFailure(string projectPath, string filePath, Exception ex, string stage)
+    {
+        var relativePath = FileIndexer.NormalizePathSeparators(Path.GetRelativePath(projectPath, filePath));
+        return new IndexFileFailure(relativePath, stage, ex.GetType().Name, ex.Message);
+    }
+
+    private sealed record IndexFileFailure(string Path, string Stage, string ExceptionType, string Message);
+
     private JsonNode ExecuteBackfillFold(JsonNode? id, JsonNode? progressToken = null)
     {
         if (!DbContext.TryValidateExistingCodeIndexDb(_dbPath, out var validationMessage, out var isNotFound))