Reduce materialization in count and graph paths

changelog.d/unreleased/3097.fixed.md

@@ -0,0 +1,18 @@
+---
+category: fixed
+issues:
+  - 3097
+affected:
+  - src/CodeIndex/Cli/QueryCommandRunner.cs
+  - src/CodeIndex/Mcp/McpToolHandlers.cs
+  - tests/CodeIndex.Tests/QueryCommandRunnerTests.cs
+  - tests/CodeIndex.Tests/McpServerTests.cs
+---
+
+## English
+
+- **Dependency JSON graph output avoids duplicate full graph array materialization (#3097)** — CLI graph output now writes JSON incrementally, and MCP graph payload construction fills bounded arrays without LINQ `ToArray` copies.
+
+## 日本語
+
+- **dependency JSON graph 出力が graph 配列全体の重複 materialization を避けるようになりました (#3097)** — CLI graph 出力は JSON を逐次書き込み、MCP graph payload は LINQ `ToArray` のコピーを作らず bounded array を構築します。

changelog.d/unreleased/3111.fixed.md

@@ -0,0 +1,16 @@
+---
+category: fixed
+issues:
+  - 3111
+affected:
+  - src/CodeIndex/Database/DbSymbolReader.cs
+  - tests/CodeIndex.Tests/DbReaderTests.cs
+---
+
+## English
+
+- **Visibility-filtered symbol and definition count queries no longer materialize full result lists (#3111)** — count-only paths apply visibility filters directly in SQL while preserving the existing result counts.
+
+## 日本語
+
+- **visibility filter 付きの symbol / definition count query が全結果リストを materialize しなくなりました (#3111)** — count-only 経路で visibility filter を SQL に直接適用し、既存の件数結果を維持します。

changelog.d/unreleased/3115.fixed.md

@@ -0,0 +1,16 @@
+---
+category: fixed
+issues:
+  - 3115
+affected:
+  - src/CodeIndex/Mcp/McpToolHandlers.cs
+  - tests/CodeIndex.Tests/McpServerTests.cs
+---
+
+## English
+
+- **MCP graph count-only handlers no longer use `int.MaxValue` row probes (#3115)** — references, callers, and callees now use total-count queries for count-only and paginated-total metadata.
+
+## 日本語
+
+- **MCP graph の count-only handler が `int.MaxValue` の行取得 probe を使わなくなりました (#3115)** — references / callers / callees は count-only と paginated total metadata に total-count query を使います。

changelog.d/unreleased/3139.fixed.md

@@ -0,0 +1,16 @@
+---
+category: fixed
+issues:
+  - 3139
+affected:
+  - src/CodeIndex/Cli/IndexFreshnessChecker.cs
+  - src/CodeIndex/Database/DbReader.cs
+---
+
+## English
+
+- **`status --check` now compares freshness without materializing the full workspace snapshot (#3139)** — indexed snapshots stream from the database, and workspace files are checked as they are scanned while unmatched indexed rows remain for missing-file classification.
+
+## 日本語
+
+- **`status --check` が workspace snapshot 全体を materialize せずに freshness を比較するようになりました (#3139)** — indexed snapshot は DB から streaming し、workspace file は scan しながら照合し、未照合の indexed row だけを missing file 分類に回します。

changelog.d/unreleased/3149.fixed.md

@@ -0,0 +1,15 @@
+---
+category: fixed
+issues:
+  - 3149
+affected:
+  - src/CodeIndex/Database/RepoMapBuilder.cs
+---
+
+## English
+
+- **Repo map now keeps bounded file-summary rankings instead of materializing every file stat before limits (#3149)** — map aggregation streams file stats, maintains top-N lists as it scans, and resolves Java module grouping without mutating a full file list.
+
+## 日本語
+
+- **repo map が limit 適用前に全 file stat を materialize せず、bounded な file-summary ranking を保持するようになりました (#3149)** — map 集約は file stat を streaming しながら top-N を更新し、Java module grouping も全 file list を mutate せずに解決します。

changelog.d/unreleased/3150.fixed.md

@@ -0,0 +1,15 @@
+---
+category: fixed
+issues:
+  - 3150
+affected:
+  - src/CodeIndex/Database/DbSymbolReader.cs
+---
+
+## English
+
+- **`unused` fallback queries no longer load every referenced symbol name into memory (#3150)** — non-SQL resolver paths now exclude referenced symbols in the candidate SQL before applying their bounded result loops.
+
+## 日本語
+
+- **`unused` fallback query が参照済み symbol 名を全件メモリへ読み込まなくなりました (#3150)** — 非 SQL resolver 経路では、bounded result loop の前に候補 SQL 側で参照済み symbol を除外します。

changelog.d/unreleased/3152.fixed.md

@@ -0,0 +1,16 @@
+---
+category: fixed
+issues:
+  - 3152
+affected:
+  - src/CodeIndex/Cli/QueryCommandRunner.cs
+  - tests/CodeIndex.Tests/QueryCommandRunnerSearchTests.cs
+---
+
+## English
+
+- **CLI structured format helpers no longer duplicate full result arrays for LSP, compact, and SARIF output (#3152)** — formatted writers now stream array items to stdout while preserving their JSON schemas.
+
+## 日本語
+
+- **CLI structured format helper が LSP / compact / SARIF 出力で全 result array を重複保持しなくなりました (#3152)** — formatted writer は JSON schema を保ったまま array item を stdout へ逐次書き込みます。

src/CodeIndex/Cli/IndexFreshnessChecker.cs

@@ -19,9 +19,6 @@ internal static IndexFreshnessCheckResult Check(DbReader reader, string? project
             };
         }
 
-        var indexed = reader.GetIndexedFileSnapshots()
-            .ToDictionary(file => file.Path, StringComparer.Ordinal);
-        var workspace = new Dictionary<string, WorkspaceFileSnapshot>(StringComparer.Ordinal);
         var indexedHeadCommit = reader.GetMetaString(DbContext.IndexedHeadCommitMetaKey);
         var indexedHeadSha = reader.GetMetaString(DbContext.IndexedHeadShaMetaKey);
         var commitScopedFreshHeadSha = reader.GetMetaString(DbContext.CommitScopedFreshHeadShaMetaKey);
@@ -43,7 +40,6 @@ internal static IndexFreshnessCheckResult Check(DbReader reader, string? project
             && !currentHeadCoveredByCommitRefresh;
         var result = new IndexFreshnessCheckResult
         {
-            IndexedFileCount = indexed.Count,
             IndexedHeadCommit = string.IsNullOrWhiteSpace(indexedHeadCommit) ? null : indexedHeadCommit,
             WorkspaceHeadCommit = string.IsNullOrWhiteSpace(workspaceHeadCommit) ? null : workspaceHeadCommit,
             HeadChanged = headChanged,
@@ -62,12 +58,50 @@ internal static IndexFreshnessCheckResult Check(DbReader reader, string? project
             AddSample(result.ScanErrors, $"{error.Path}: {error.Message}");
         }
 
-        foreach (var absolutePath in scan.Files.OrderBy(path => path, StringComparer.Ordinal))
+        using var indexedEnumerator = reader.EnumerateIndexedFileSnapshots().GetEnumerator();
+        var hasIndexed = MoveNextIndexed();
+        var skipWorktreePathsLoaded = false;
+        HashSet<string>? skipWorktreePaths = null;
+
+        foreach (var absolutePath in scan.Files.OrderBy(path => FileIndexer.NormalizeIndexPath(Path.GetRelativePath(projectRoot, path)), StringComparer.Ordinal))
         {
             try
             {
                 var (record, _, _, _) = indexer.BuildRecordWithRawBytes(absolutePath);
-                workspace[record.Path] = new WorkspaceFileSnapshot(record.Checksum ?? string.Empty, record.Lines);
+                result.WorkspaceFileCount++;
+                while (hasIndexed && string.Compare(indexedEnumerator.Current.Path, record.Path, StringComparison.Ordinal) < 0)
+                {
+                    AddMissingIndexedPath(indexedEnumerator.Current.Path);
+                    hasIndexed = MoveNextIndexed();
+                }
+
+                if (!hasIndexed || string.Compare(indexedEnumerator.Current.Path, record.Path, StringComparison.Ordinal) > 0)
+                {
+                    result.UnindexedFileCount++;
+                    AddSample(result.UnindexedFiles, record.Path);
+                    continue;
+                }
+
+                var indexedFile = indexedEnumerator.Current;
+                if (string.IsNullOrWhiteSpace(indexedFile.Checksum))
+                {
+                    result.UnverifiableFileCount++;
+                    AddSample(result.UnverifiableFiles, record.Path);
+                    hasIndexed = MoveNextIndexed();
+                    continue;
+                }
+
+                if (!string.Equals(indexedFile.Checksum, record.Checksum ?? string.Empty, StringComparison.OrdinalIgnoreCase)
+                    || (indexedFile.Lines.HasValue && indexedFile.Lines.Value != record.Lines))
+                {
+                    result.ChangedFileCount++;
+                    AddSample(result.ChangedFiles, record.Path);
+                    hasIndexed = MoveNextIndexed();
+                    continue;
+                }
+
+                result.MatchedFileCount++;
+                hasIndexed = MoveNextIndexed();
             }
             catch (Exception ex) when (ex is IOException or UnauthorizedAccessException or InvalidOperationException)
             {
@@ -77,52 +111,44 @@ internal static IndexFreshnessCheckResult Check(DbReader reader, string? project
             }
         }
 
-        result.WorkspaceFileCount = workspace.Count;
-
-        foreach (var (path, workspaceFile) in workspace.OrderBy(kv => kv.Key, StringComparer.Ordinal))
+        while (hasIndexed)
         {
-            if (!indexed.TryGetValue(path, out var indexedFile))
-            {
-                result.UnindexedFileCount++;
-                AddSample(result.UnindexedFiles, path);
-                continue;
-            }
-
-            if (string.IsNullOrWhiteSpace(indexedFile.Checksum))
-            {
-                result.UnverifiableFileCount++;
-                AddSample(result.UnverifiableFiles, path);
-                continue;
-            }
+            AddMissingIndexedPath(indexedEnumerator.Current.Path);
+            hasIndexed = MoveNextIndexed();
+        }
 
-            if (!string.Equals(indexedFile.Checksum, workspaceFile.Checksum, StringComparison.OrdinalIgnoreCase)
-                || (indexedFile.Lines.HasValue && indexedFile.Lines.Value != workspaceFile.Lines))
-            {
-                result.ChangedFileCount++;
-                AddSample(result.ChangedFiles, path);
-                continue;
-            }
+        result.Checked = result.ScanErrorCount == 0;
+        result.MatchesWorkspace = result.Checked
+            && !result.HeadChanged
+            && result.ChangedFileCount == 0
+            && result.MissingFileCount == 0
+            && result.UnindexedFileCount == 0
+            && result.UnverifiableFileCount == 0;
+        result.Reason = BuildReason(result);
+        return result;
 
-            result.MatchedFileCount++;
+        bool MoveNextIndexed()
+        {
+            var moved = indexedEnumerator.MoveNext();
+            if (moved)
+                result.IndexedFileCount++;
+            return moved;
         }
 
-        var missingCandidates = indexed.Keys
-            .Except(workspace.Keys, StringComparer.Ordinal)
-            .OrderBy(path => path, StringComparer.Ordinal)
-            .ToList();
-
-        // Skip-worktree paths are intentionally absent from disk (sparse-checkout cone/non-cone,
-        // partial clone, or manual update-index --skip-worktree). Reclassify them so the freshness
-        // gate stops flagging them as "missing" and rebuilds.
-        // skip-worktree のパスは意図的に worktree から外されている(sparse-checkout cone/non-cone、
-        // partial clone、手動の update-index --skip-worktree)。これらを "missing" から切り分け、
-        // 不要な rebuild トリガーを止める。
-        HashSet<string>? skipWorktreePaths = null;
-        if (missingCandidates.Count > 0)
-            skipWorktreePaths = GitHelper.TryGetSkipWorktreePaths(projectRoot);
-
-        foreach (var path in missingCandidates)
+        void AddMissingIndexedPath(string path)
         {
+            // Skip-worktree paths are intentionally absent from disk (sparse-checkout cone/non-cone,
+            // partial clone, or manual update-index --skip-worktree). Reclassify them so the freshness
+            // gate stops flagging them as "missing" and rebuilds.
+            // skip-worktree のパスは意図的に worktree から外されている(sparse-checkout cone/non-cone、
+            // partial clone、手動の update-index --skip-worktree)。これらを "missing" から切り分け、
+            // 不要な rebuild トリガーを止める。
+            if (!skipWorktreePathsLoaded)
+            {
+                skipWorktreePaths = GitHelper.TryGetSkipWorktreePaths(projectRoot);
+                skipWorktreePathsLoaded = true;
+            }
+
             if (skipWorktreePaths != null && skipWorktreePaths.Contains(path))
             {
                 result.OutsideSparseConeFileCount++;
@@ -134,16 +160,6 @@ internal static IndexFreshnessCheckResult Check(DbReader reader, string? project
                 AddSample(result.MissingFiles, path);
             }
         }
-
-        result.Checked = result.ScanErrorCount == 0;
-        result.MatchesWorkspace = result.Checked
-            && !result.HeadChanged
-            && result.ChangedFileCount == 0
-            && result.MissingFileCount == 0
-            && result.UnindexedFileCount == 0
-            && result.UnverifiableFileCount == 0;
-        result.Reason = BuildReason(result);
-        return result;
     }
 
     private static string BuildReason(IndexFreshnessCheckResult result)
@@ -175,6 +191,4 @@ private static void AddSample(List<string> samples, string value)
         if (samples.Count < SampleLimit)
             samples.Add(value);
     }
-
-    private readonly record struct WorkspaceFileSnapshot(string Checksum, int Lines);
 }