[codex] Fix issues 3681, 3683, 3689, 3690, 3715

changelog.d/unreleased/3681.fixed.md

@@ -0,0 +1,18 @@
+---
+category: fixed
+issues:
+  - 3681
+affected:
+  - src/CodeIndex/Mcp/BoundedJsonUtf8Stream.cs
+  - src/CodeIndex/Mcp/McpServer.cs
+  - src/CodeIndex/Mcp/AuditLogSink.cs
+  - tests/CodeIndex.Tests/McpServerTests.cs
+---
+
+## English
+
+- **MCP JSON byte-limit streams are shared across response and audit-log serialization (#3681)** — bounded UTF-8 serialization now uses one helper with tests for unsupported stream operations and partial byte-limit capture.
+
+## 日本語
+
+- **MCP の JSON バイト制限 stream を response と audit-log serialization で共有しました (#3681)** — bounded UTF-8 serialization は 1 つの helper を使うようになり、未対応 stream 操作と byte limit 超過時の部分 capture をテストで固定しました。

changelog.d/unreleased/3683.fixed.md

@@ -0,0 +1,24 @@
+---
+category: fixed
+issues:
+  - 3683
+affected:
+  - src/CodeIndex/Cli/CommandErrorWriter.cs
+  - src/CodeIndex/Cli/QueryCommandRunner.cs
+  - src/CodeIndex/Cli/ProgramRunner.cs
+  - src/CodeIndex/Cli/IndexCommandRunner.Parse.cs
+  - src/CodeIndex/Mcp/McpServer.cs
+  - src/CodeIndex/Database/DbDebug.cs
+  - src/CodeIndex/Diagnostics/BackgroundTaskObserver.cs
+  - src/CodeIndex/Indexer/Extensibility/ExtractorPluginRegistry.Diagnostics.cs
+  - tests/CodeIndex.Tests/HookCommandRunnerTests.cs
+  - tests/CodeIndex.Tests/DbDebugTests.cs
+---
+
+## English
+
+- **Command-facing stderr diagnostics now use the shared CLI error writer (#3683)** — direct stderr writes are centralized behind `CommandErrorWriter`, with tests covering JSON-mode error isolation and redacted diagnostics.
+
+## 日本語
+
+- **コマンド向け stderr 診断が shared CLI error writer を使うようになりました (#3683)** — direct stderr write は `CommandErrorWriter` に集約し、JSON mode の error 分離と redacted diagnostic をテストで固定しました。

changelog.d/unreleased/3689.fixed.md

@@ -0,0 +1,20 @@
+---
+category: fixed
+issues:
+  - 3689
+affected:
+  - src/CodeIndex/Indexer/Scanning/FileWriteProbe.cs
+  - src/CodeIndex/Indexer/Scanning/FileIndexer.cs
+  - src/CodeIndex/Cli/GitHelper.cs
+  - src/CodeIndex/Cli/PathCasing.cs
+  - src/CodeIndex/Cli/GlobalToolLog.cs
+  - tests/CodeIndex.Tests/FileIndexerTests.cs
+---
+
+## English
+
+- **Filesystem write probes now share long-path-safe create/delete behavior (#3689)** — case-sensitivity probes and global log directory checks now use one helper, with tests that verify successful cleanup and failure reporting.
+
+## 日本語
+
+- **filesystem write probe が long-path-safe な作成・削除処理を共有するようになりました (#3689)** — case-sensitivity probe と global log directory check は 1 つの helper を使い、成功時 cleanup と失敗報告をテストで確認します。

changelog.d/unreleased/3690.changed.md

@@ -0,0 +1,25 @@
+---
+category: changed
+issues:
+  - 3690
+affected:
+  - src/CodeIndex/Cli/CdidxConfigFile.cs
+  - src/CodeIndex/Cli/ConsoleUi.cs
+  - src/CodeIndex/Cli/GlobalToolLog.cs
+  - src/CodeIndex/Cli/ProgramRunner.cs
+  - src/CodeIndex/Cli/SearchAuditRecipes.cs
+  - src/CodeIndex/Cli/UpdateChecker.cs
+  - src/CodeIndex/Database/DbReader.cs
+  - src/CodeIndex/Indexer/Scanning/FileIndexer.cs
+  - tests/CodeIndex.Tests/ConsoleUiTests.cs
+  - tests/CodeIndex.Tests/GlobalToolLogTests.cs
+  - tests/CodeIndex.Tests/ProgramRunnerTests.cs
+---
+
+## English
+
+- **CLI environment variable reads now use scoped `CdidxEnvironment` overrides more consistently (#3690)** — config loading, console policy, logging, update checks, recipe discovery, fold diagnostics, and index file-size limits can be tested without mutating process-global environment variables.
+
+## 日本語
+
+- **CLI の環境変数読み取りが scoped な `CdidxEnvironment` override をより一貫して使うようになりました (#3690)** — config loading、console policy、logging、update check、recipe discovery、fold diagnostics、index file-size limit は process-global な環境変数を変更せずにテストできます。

changelog.d/unreleased/3715.fixed.md

@@ -0,0 +1,16 @@
+---
+category: fixed
+issues:
+  - 3715
+affected:
+  - src/CodeIndex/Cli/ExportImportCommandRunner.cs
+  - tests/CodeIndex.Tests/ExportImportCommandRunnerTests.cs
+---
+
+## English
+
+- **Export manifests now report unknown-extension sample list limits explicitly (#3715)** — archives include sample count, limit, and truncation metadata while preserving existing unknown-extension fields for older import/export compatibility.
+
+## 日本語
+
+- **export manifest が unknown-extension sample list の制限を明示するようになりました (#3715)** — archive は sample count、limit、truncation metadata を含み、既存の unknown-extension field は古い import/export 互換性のため維持します。

src/CodeIndex/Cli/ActiveWorkspace.cs

@@ -247,5 +247,5 @@ private static bool IsFullyQualifiedPath(string path)
     };
 
     private static void WriteLoadWarning(string source, string reason)
-        => Console.Error.WriteLine($"[cdidx] Ignoring active workspace {source}: {ConsoleUi.FormatBoundedValue(reason)}. Hint: inspect or reset the active workspace configuration.");
+        => CommandErrorWriter.WriteStderr($"[cdidx] Ignoring active workspace {source}: {ConsoleUi.FormatBoundedValue(reason)}. Hint: inspect or reset the active workspace configuration.");
 }

src/CodeIndex/Cli/CdidxConfigFile.cs

@@ -88,7 +88,7 @@ internal sealed record LoadResult(string? Path, string? Error)
     /// validation errors. No-op when `CDIDX_DISABLE_CONFIG_FILE=1` is set.
     /// </summary>
     internal static LoadResult Load(string startingDirectory)
-        => Load(startingDirectory, Environment.GetEnvironmentVariable);
+        => Load(startingDirectory, CdidxEnvironment.GetEnvironmentVariable);
 
     internal static LoadResult Load(
         string startingDirectory,
@@ -529,7 +529,7 @@ internal static int RunValidate(string[] args, JsonSerializerOptions jsonOptions
         var result = Load(Environment.CurrentDirectory, name => name == DisableEnvVar ? null : Environment.GetEnvironmentVariable(name));
         if (result.Failed)
         {
-            Console.Error.WriteLine(result.Error);
+            CommandErrorWriter.WriteStderr(result.Error);
             return CommandExitCodes.UsageError;
         }
 

src/CodeIndex/Cli/CodeIndexExceptionFormatter.cs

@@ -34,11 +34,11 @@ public static void Write(CodeIndexException ex, string[] args, JsonSerializerOpt
         // QueryCommandRunner / IndexCommandRunner already emit so downstream
         // parsers do not need a second format.
         // 既存の `Error [Exxx]: ...` 形に揃え、parser の差分を最小化する。
-        Console.Error.WriteLine($"Error [{ex.Code}]: {ex.Message}");
+        CommandErrorWriter.WriteStderr($"Error [{ex.Code}]: {ex.Message}");
         if (!string.IsNullOrEmpty(ex.Path))
-            Console.Error.WriteLine($"Path: {ex.Path}");
+            CommandErrorWriter.WriteStderr($"Path: {ex.Path}");
         if (!string.IsNullOrEmpty(ex.Hint))
-            Console.Error.WriteLine($"Hint: {ex.Hint}");
+            CommandErrorWriter.WriteStderr($"Hint: {ex.Hint}");
     }
 
     internal static bool HasJsonFlag(string[] args)

src/CodeIndex/Cli/CommandErrorWriter.cs

@@ -10,7 +10,7 @@ internal static class CommandErrorWriter
     internal static void WriteStdout(string message = "")
         => Console.WriteLine(message);
 
-    internal static void WriteStderr(string message = "")
+    internal static void WriteStderr(string? message = "")
         => Console.Error.WriteLine(message);
 
     internal static void WriteWarning(string message)

src/CodeIndex/Cli/ConsoleUi.cs

@@ -247,9 +247,9 @@ internal static void TryWriteErrorLine(string? value = null)
         try
         {
             if (value == null)
-                Console.Error.WriteLine();
+                CommandErrorWriter.WriteStderr();
             else
-                Console.Error.WriteLine(value);
+                CommandErrorWriter.WriteStderr(value);
         }
         catch (ObjectDisposedException)
         {
@@ -390,7 +390,7 @@ internal static bool ShouldUseProgressAnimation()
         if (IsTruthyEnvironmentVariable(DisableProgressEnvironmentVariable))
             return false;
 
-        var reducedMotion = Environment.GetEnvironmentVariable(PrefersReducedMotionEnvironmentVariable);
+        var reducedMotion = CdidxEnvironment.GetEnvironmentVariable(PrefersReducedMotionEnvironmentVariable);
         return string.IsNullOrWhiteSpace(reducedMotion) || !IsTruthyEnvironmentValue(reducedMotion);
     }
 
@@ -592,7 +592,7 @@ public static void PrintWarning(string message)
         lock (TerminalLock)
         {
             ClearProgressLineCore();
-            Console.Error.WriteLine($"  [WARN] {message}");
+            CommandErrorWriter.WriteStderr($"  [WARN] {message}");
             Console.Error.Flush();
             Console.Out.Flush();
         }
@@ -1401,7 +1401,7 @@ public static bool PrintCompletions(string shell)
         }
         catch (ArgumentOutOfRangeException)
         {
-            Console.Error.WriteLine($"Unknown shell: {shell}. Supported: bash, zsh, fish, powershell");
+            CommandErrorWriter.WriteStderr($"Unknown shell: {shell}. Supported: bash, zsh, fish, powershell");
             return false;
         }
     }
@@ -1941,7 +1941,7 @@ public static ColorPalette ResolveColorPalette()
         if (_explicitPalette is { } explicitPalette)
             return explicitPalette;
 
-        var envPalette = Environment.GetEnvironmentVariable("CDIDX_COLOR_PALETTE");
+        var envPalette = CdidxEnvironment.GetEnvironmentVariable("CDIDX_COLOR_PALETTE");
         if (!string.IsNullOrWhiteSpace(envPalette) && TryParseColorPalette(envPalette, out var parsed))
             return parsed;
 
@@ -1957,15 +1957,15 @@ public static ColorPalette ResolveColorPalette()
     /// </summary>
     internal static ColorPalette DetectColorPalette()
     {
-        var colorTerm = Environment.GetEnvironmentVariable("COLORTERM");
+        var colorTerm = CdidxEnvironment.GetEnvironmentVariable("COLORTERM");
         if (!string.IsNullOrEmpty(colorTerm))
         {
             var ct = colorTerm.Trim().ToLowerInvariant();
             if (ct == "truecolor" || ct == "24bit")
                 return ColorPalette.Truecolor;
         }
 
-        var term = Environment.GetEnvironmentVariable("TERM");
+        var term = CdidxEnvironment.GetEnvironmentVariable("TERM");
         if (!string.IsNullOrEmpty(term))
         {
             var t = term.ToLowerInvariant();
@@ -2159,14 +2159,14 @@ public static bool ShouldUseColor()
 
     private static bool HasTerminalEnvironmentHint()
     {
-        if (!string.IsNullOrEmpty(Environment.GetEnvironmentVariable("WT_SESSION")))
+        if (!string.IsNullOrEmpty(CdidxEnvironment.GetEnvironmentVariable("WT_SESSION")))
             return true;
-        if (!string.IsNullOrEmpty(Environment.GetEnvironmentVariable("WT_PROFILE_ID")))
+        if (!string.IsNullOrEmpty(CdidxEnvironment.GetEnvironmentVariable("WT_PROFILE_ID")))
             return true;
-        if (!string.IsNullOrEmpty(Environment.GetEnvironmentVariable("TERM_PROGRAM")))
+        if (!string.IsNullOrEmpty(CdidxEnvironment.GetEnvironmentVariable("TERM_PROGRAM")))
             return true;
 
-        var term = Environment.GetEnvironmentVariable("TERM");
+        var term = CdidxEnvironment.GetEnvironmentVariable("TERM");
         return !string.IsNullOrWhiteSpace(term)
             && !term.Equals("dumb", StringComparison.OrdinalIgnoreCase);
     }
@@ -2176,7 +2176,7 @@ private static bool IsTerminalEnvironmentDisabled()
 
     private static bool IsCiEnvironment()
     {
-        var ci = Environment.GetEnvironmentVariable("CI");
+        var ci = CdidxEnvironment.GetEnvironmentVariable("CI");
         return !string.IsNullOrEmpty(ci)
             && !ci.Equals("0", StringComparison.OrdinalIgnoreCase)
             && !ci.Equals("false", StringComparison.OrdinalIgnoreCase)
@@ -2227,17 +2227,17 @@ internal static void ResetTerminalCapabilityCacheForTests()
 
     private static bool IsForceColorRequested()
     {
-        var force = Environment.GetEnvironmentVariable("CLICOLOR_FORCE");
+        var force = CdidxEnvironment.GetEnvironmentVariable("CLICOLOR_FORCE");
         return !string.IsNullOrEmpty(force) && force != "0";
     }
 
     private static bool IsNoColorRequested()
     {
-        var noColor = Environment.GetEnvironmentVariable("NO_COLOR");
+        var noColor = CdidxEnvironment.GetEnvironmentVariable("NO_COLOR");
         if (!string.IsNullOrEmpty(noColor))
             return true;
 
-        var cliColor = Environment.GetEnvironmentVariable("CLICOLOR");
+        var cliColor = CdidxEnvironment.GetEnvironmentVariable("CLICOLOR");
         return cliColor == "0";
     }
 
@@ -2262,29 +2262,29 @@ private static bool IsAsciiOutputRequested()
         if (_asciiOutputForced)
             return true;
 
-        var ascii = Environment.GetEnvironmentVariable("CDIDX_ASCII");
+        var ascii = CdidxEnvironment.GetEnvironmentVariable("CDIDX_ASCII");
         if (!string.IsNullOrEmpty(ascii) && ascii != "0")
             return true;
 
-        var noUnicode = Environment.GetEnvironmentVariable("NO_UNICODE");
+        var noUnicode = CdidxEnvironment.GetEnvironmentVariable("NO_UNICODE");
         if (!string.IsNullOrEmpty(noUnicode) && noUnicode != "0")
             return true;
 
-        var atBridgeType = Environment.GetEnvironmentVariable("AT_BRIDGE_TYPE");
+        var atBridgeType = CdidxEnvironment.GetEnvironmentVariable("AT_BRIDGE_TYPE");
         if (!string.IsNullOrEmpty(atBridgeType))
             return true;
 
-        var accessibilityEnabled = Environment.GetEnvironmentVariable("ACCESSIBILITY_ENABLED");
+        var accessibilityEnabled = CdidxEnvironment.GetEnvironmentVariable("ACCESSIBILITY_ENABLED");
         if (!string.IsNullOrEmpty(accessibilityEnabled) && accessibilityEnabled != "0")
             return true;
 
-        return IsPosixLocale(Environment.GetEnvironmentVariable("LC_ALL"))
-            || IsPosixLocale(Environment.GetEnvironmentVariable("LC_CTYPE"))
-            || IsPosixLocale(Environment.GetEnvironmentVariable("LANG"));
+        return IsPosixLocale(CdidxEnvironment.GetEnvironmentVariable("LC_ALL"))
+            || IsPosixLocale(CdidxEnvironment.GetEnvironmentVariable("LC_CTYPE"))
+            || IsPosixLocale(CdidxEnvironment.GetEnvironmentVariable("LANG"));
     }
 
     private static bool IsTruthyEnvironmentVariable(string name)
-        => IsTruthyEnvironmentValue(Environment.GetEnvironmentVariable(name));
+        => IsTruthyEnvironmentValue(CdidxEnvironment.GetEnvironmentVariable(name));
 
     private static bool IsTruthyEnvironmentValue(string? value)
     {
@@ -2295,7 +2295,7 @@ private static bool IsTruthyEnvironmentValue(string? value)
     }
 
     private static bool IsDumbTerminal()
-        => string.Equals(Environment.GetEnvironmentVariable("TERM"), "dumb", StringComparison.OrdinalIgnoreCase);
+        => string.Equals(CdidxEnvironment.GetEnvironmentVariable("TERM"), "dumb", StringComparison.OrdinalIgnoreCase);
 
     private static bool IsPosixLocale(string? locale)
         => locale != null
@@ -2310,7 +2310,7 @@ private static bool IsUnicodeLocale(string locale)
     {
         foreach (var name in names)
         {
-            var value = Environment.GetEnvironmentVariable(name);
+            var value = CdidxEnvironment.GetEnvironmentVariable(name);
             if (!string.IsNullOrEmpty(value))
                 return value;
         }
@@ -2359,7 +2359,7 @@ private static int GetFallbackWindowWidth(Exception? exception)
         if (_traceWidthDetectionFailures && !_widthDetectionTraceWritten)
         {
             var suffix = exception == null ? string.Empty : $" ({exception.GetType().Name}: {exception.Message})";
-            Console.Error.WriteLine($"cdidx: console width detection failed; using COLUMNS or 80 columns{suffix}");
+            CommandErrorWriter.WriteStderr($"cdidx: console width detection failed; using COLUMNS or 80 columns{suffix}");
             _widthDetectionTraceWritten = true;
         }
 
@@ -2368,7 +2368,7 @@ private static int GetFallbackWindowWidth(Exception? exception)
 
     private static bool TryGetColumnsEnvironmentWidth(out int width)
     {
-        var columns = Environment.GetEnvironmentVariable("COLUMNS");
+        var columns = CdidxEnvironment.GetEnvironmentVariable("COLUMNS");
         if (int.TryParse(columns, NumberStyles.Integer, CultureInfo.InvariantCulture, out width) && width > 0)
             return true;
 

src/CodeIndex/Cli/DbCommandRunner.cs

@@ -292,7 +292,7 @@ private static int RunPrune(DbCommandOptions options, JsonSerializerOptions json
                 Console.WriteLine($"  orphan symbols           : {result.OrphanSymbols:N0}");
                 Console.WriteLine($"  total                    : {result.Total:N0}");
                 foreach (var warning in result.Warnings)
-                    Console.Error.WriteLine($"Warning [{warning.Code}]: {warning.Message}");
+                    CommandErrorWriter.WriteStderr($"Warning [{warning.Code}]: {warning.Message}");
             }
 
             return CommandExitCodes.Success;
@@ -391,7 +391,7 @@ private static int RunListCheckpoints(DbCommandOptions options, JsonSerializerOp
             }
 
             foreach (var diagnostic in result.Diagnostics)
-                Console.Error.WriteLine($"Warning [{diagnostic.Code}]: {diagnostic.Message}");
+                CommandErrorWriter.WriteStderr($"Warning [{diagnostic.Code}]: {diagnostic.Message}");
         }
 
         return CommandExitCodes.Success;
@@ -962,7 +962,7 @@ private static string RestoreCheckpoint(string fullDbPath, string name, string c
             }
             catch (Exception rollbackEx) when (IsRecoverableRestoreException(rollbackEx))
             {
-                Console.Error.WriteLine($"Warning: failed to roll back database restore from backup {ConsoleUi.FormatBoundedValue(backupPath)} ({CommandErrorWriter.FormatSanitizedException(rollbackEx)}).");
+                CommandErrorWriter.WriteStderr($"Warning: failed to roll back database restore from backup {ConsoleUi.FormatBoundedValue(backupPath)} ({CommandErrorWriter.FormatSanitizedException(rollbackEx)}).");
             }
 
             throw;
@@ -1070,7 +1070,7 @@ internal static void TryDeleteTemporaryDirectory(string path, string cleanupDesc
         {
             if (!TryValidateTemporaryDirectoryCleanupTarget(path, safeRoot, expectedNamePrefix, out var fullPath, out var validationFailure))
             {
-                Console.Error.WriteLine($"Warning: skipped deleting {cleanupDescription} {ConsoleUi.FormatBoundedValue(path)} ({validationFailure}).");
+                CommandErrorWriter.WriteStderr($"Warning: skipped deleting {cleanupDescription} {ConsoleUi.FormatBoundedValue(path)} ({validationFailure}).");
                 return;
             }
 

src/CodeIndex/Cli/DiffCommandRunner.cs

@@ -840,9 +840,9 @@ private static int WriteCommandError(bool json, JsonSerializerOptions jsonOption
                 CliJsonSerializerContextFactory.Create(jsonOptions).CommandErrorJsonResult));
         else
         {
-            Console.Error.WriteLine($"Error [{errorCode ?? CommandErrorCodes.UsageError}]: {message}");
+            CommandErrorWriter.WriteStderr($"Error [{errorCode ?? CommandErrorCodes.UsageError}]: {message}");
             if (!string.IsNullOrWhiteSpace(hint))
-                Console.Error.WriteLine($"Hint: {hint}");
+                CommandErrorWriter.WriteStderr($"Hint: {hint}");
         }
         return exitCode;
     }