[codex] Fix search recipe and export issue workflows

changelog.d/unreleased/3667.changed.md

@@ -0,0 +1,18 @@
+---
+category: changed
+issues:
+  - 3667
+affected:
+  - src/CodeIndex/Cli/SearchAuditRecipes.cs
+  - src/CodeIndex/Cli/QueryCommandRunner.cs
+  - tests/CodeIndex.Tests/QueryCommandRunnerSearchTests.cs
+  - USER_GUIDE.md
+---
+
+## English
+
+- **Recipe JSON output now includes bounded run summaries (#3667)** — recipe JSON and compact responses report per-query limits, emitted/truncated counts, minimum omitted counts, and cursor availability so large audit runs can be paged intentionally.
+
+## 日本語
+
+- **recipe JSON output に bounded run summary を追加しました (#3667)** — recipe JSON と compact response は query ごとの limit、emitted/truncated count、最小 omitted count、cursor 利用可否を返し、大きな audit run を意図的に page できるようにしました。

changelog.d/unreleased/3668.changed.md

@@ -0,0 +1,18 @@
+---
+category: changed
+issues:
+  - 3668
+affected:
+  - src/CodeIndex/Cli/QueryCommandRunner.cs
+  - src/CodeIndex/Cli/SearchAuditRecipes.cs
+  - src/CodeIndex/Cli/SuggestionsCommandRunner.cs
+  - src/CodeIndex/Cli/JsonOutputContracts.cs
+  - tests/CodeIndex.Tests/QueryCommandRunnerSearchTests.cs
+  - tests/CodeIndex.Tests/ProgramCliTests.cs
+  - USER_GUIDE.md
+---
+## English
+- **Issue-draft exports now include triage metadata (#3668)** - Search and suggestion issue-draft JSON now expose severity, confidence, evidence count, and duplicate guidance, and generated bodies include the same metadata before filing guidance.
+
+## 日本語
+- **Issue draft export に triage metadata を追加 (#3668)** - search と suggestions の issue-draft JSON が severity、confidence、evidence count、duplicate guidance を出力し、生成 body にも起票前確認用の同じ metadata を含めるようになりました。

changelog.d/unreleased/3807.changed.md

@@ -0,0 +1,16 @@
+---
+category: changed
+issues:
+  - 3807
+affected:
+  - src/CodeIndex/Cli/SearchAuditRecipes.cs
+  - tests/CodeIndex.Tests/QueryCommandRunnerSearchTests.cs
+---
+
+## English
+
+- **External search recipes now honor declared defaults and hide raw source paths in diagnostics (#3807)** — `default_scope`, `default_path_patterns`, and `default_exclude_paths` are applied to recipe runs, while load diagnostics identify configured recipe sources by ordinal label instead of echoing filesystem paths.
+
+## 日本語
+
+- **外部検索レシピの defaults を反映し、診断で生の source path を隠すようになりました (#3807)** — `default_scope`、`default_path_patterns`、`default_exclude_paths` を recipe 実行に適用し、読み込み診断では filesystem path をそのまま出さず番号付き source label で識別します。

changelog.d/unreleased/3826-3674.changed.md

@@ -0,0 +1,21 @@
+---
+category: changed
+issues:
+  - 3826
+  - 3674
+affected:
+  - src/CodeIndex/Cli/CdidxConfigFile.cs
+  - src/CodeIndex/Cli/SearchAuditRecipes.cs
+  - src/CodeIndex/Cli/QueryCommandRunner.cs
+  - tests/CodeIndex.Tests/CdidxConfigFileTests.cs
+  - tests/CodeIndex.Tests/QueryCommandRunnerSearchTests.cs
+  - USER_GUIDE.md
+---
+
+## English
+
+- **Search recipe and config discovery boundaries are stricter (#3826, #3674)** — external recipe sources are read through a bounded helper, recipe queries can declare severity plus query-local include/exclude globs while still honoring explicit user `--path` filters, built-in audit recipes cover additional IO/sleep/HTTP patterns, and project config discovery stops at repository/workspace boundaries.
+
+## 日本語
+
+- **検索レシピと設定探索の境界を強化しました (#3826, #3674)** — 外部 recipe source は bounded helper 経由で読み込み、recipe query は severity と query-local include/exclude glob を宣言しつつ明示的なユーザー `--path` filter も尊重し、built-in audit recipe は追加の IO/sleep/HTTP pattern を扱い、project config discovery は repository/workspace boundary で停止します。

changelog.d/unreleased/3827.changed.md

@@ -0,0 +1,22 @@
+---
+category: changed
+issues:
+  - 3827
+affected:
+  - src/CodeIndex/Cli/IssueDuplicatePreflight.cs
+  - src/CodeIndex/Cli/QueryCommandRunner.cs
+  - src/CodeIndex/Cli/SuggestionsCommandRunner.cs
+  - src/CodeIndex/Cli/CliFlagSchema.cs
+  - src/CodeIndex/Cli/ConsoleUi.cs
+  - tests/CodeIndex.Tests/QueryCommandRunnerSearchTests.cs
+  - tests/CodeIndex.Tests/ProgramCliTests.cs
+  - tests/CodeIndex.Tests/ConsoleUiTests.cs
+  - USER_GUIDE.md
+---
+## English
+- **Machine-readable search exports carry richer metadata (#3827)** - Search CSV/TSV output now includes query, language, visibility, enclosing symbol, match line, and recipe/query columns, while SARIF output includes rule metadata, help text, result levels, and normalized artifact URIs.
+- **Issue-draft duplicate preflight is tunable (#3827)** - Search and suggestion issue-draft exports accept duplicate confidence presets or an explicit score threshold and report the effective confidence/minimum score in JSON.
+
+## 日本語
+- **機械可読 search export の metadata を拡充 (#3827)** - search の CSV/TSV 出力に query、language、visibility、enclosing symbol、match line、recipe/query 列を追加し、SARIF 出力には rule metadata、help text、result level、正規化済み artifact URI を含めるようにしました。
+- **Issue draft の duplicate preflight を調整可能にしました (#3827)** - search と suggestions の issue-draft export が duplicate confidence preset または明示的な score threshold を受け取り、有効な confidence / minimum score を JSON に出力します。

src/CodeIndex/Cli/CdidxConfigFile.cs

@@ -64,6 +64,12 @@ internal static class CdidxConfigFile
     private static readonly IReadOnlyList<string> KnownMcpKeys = new[] { "tools", "rate_limit" };
     private static readonly IReadOnlyList<string> KnownMcpToolsKeys = new[] { "allow", "deny" };
     private static readonly IReadOnlyList<string> KnownMcpRateLimitKeys = new[] { "rps", "burst", "bucket_idle_seconds" };
+    private static readonly IReadOnlyList<string> ConfigDiscoveryBoundaryDirectories = new[] { ".git", ".hg", ".svn" };
+    private static readonly IReadOnlyList<string> ConfigDiscoveryBoundaryFiles = new[]
+    {
+        WorkspaceManifestLoader.FileName,
+        WorkspaceManifestLoader.DotFileName,
+    };
 
     internal sealed record LoadResult(string? Path, string? Error)
     {
@@ -465,11 +471,32 @@ private static (IReadOnlyDictionary<string, string> Settings, IReadOnlyDictionar
             var candidate = Path.Combine(current.FullName, FileName);
             if (File.Exists(LongPath.EnsureWindowsPrefix(candidate)))
                 return candidate;
+            if (IsConfigDiscoveryBoundary(current))
+                break;
             current = current.Parent;
         }
         return null;
     }
 
+    private static bool IsConfigDiscoveryBoundary(DirectoryInfo directory)
+    {
+        foreach (var directoryName in ConfigDiscoveryBoundaryDirectories)
+        {
+            var path = Path.Combine(directory.FullName, directoryName);
+            if (Directory.Exists(LongPath.EnsureWindowsPrefix(path)))
+                return true;
+        }
+
+        foreach (var fileName in ConfigDiscoveryBoundaryFiles)
+        {
+            var path = Path.Combine(directory.FullName, fileName);
+            if (File.Exists(LongPath.EnsureWindowsPrefix(path)))
+                return true;
+        }
+
+        return false;
+    }
+
     private static string ResolveConfigWorkspaceRoot(string configPath)
     {
         var fullConfigPath = Path.GetFullPath(configPath);

src/CodeIndex/Cli/CliFlagSchema.cs

@@ -289,6 +289,8 @@ private static IReadOnlyList<CliFlag> BuildAll()
             new() { Name = "--named-query", ValuePlaceholder = "<name>=<query>", Description = "Search: add one named ad hoc batch query", Commands = Set("search") },
             new() { Name = "--open-issues", ValuePlaceholder = "<path|github|github:owner/name>", Description = "Preflight issue drafts against open issue JSON or GitHub open issues", Commands = Set("search", "suggestions") },
             new() { Name = "--repo", ValuePlaceholder = "<owner/name>", Description = "Issue-drafts: GitHub repository for --open-issues github", Commands = Set("search", "suggestions") },
+            new() { Name = "--duplicate-confidence", ValuePlaceholder = "<low|medium|high>", Description = "Issue-drafts: preset duplicate-preflight match threshold", Commands = Set("search", "suggestions") },
+            new() { Name = "--duplicate-threshold", ValuePlaceholder = "<score>", Description = "Issue-drafts: explicit duplicate-preflight minimum score from 0 to 1", Commands = Set("search", "suggestions") },
             new() { Name = "--issue-title", ValuePlaceholder = "<title>", Description = "Search issue-drafts: override the title for an ad hoc search draft", Commands = Set("search") },
             new() { Name = "--issue-label", ValuePlaceholder = "<label>", Description = "Search issue-drafts: add a label hint; repeat or comma-separate values", Commands = Set("search") },
             new() { Name = "--cursor", ValuePlaceholder = "<cursor>", Description = "Search recipe: pagination cursor returned as next_cursor", Commands = Set("search") },

src/CodeIndex/Cli/ConsoleUi.cs

@@ -88,7 +88,7 @@ private static readonly (string Command, string Usage)[] CommandUsageLines =
         ("index-commits", "cdidx index <projectPath> --commits <commit-ref> [commit-ref ...] [--db <path>] [--verbose] [--dry-run] [--json] [--memory-trace] [--duration-format <auto|seconds|hms>] [--max-file-bytes <bytes>] [--include-symbol-kind <kind>[,<kind>]] [--exclude-symbol-kind <kind>[,<kind>]]"),
         ("index-changed-between", "cdidx index <projectPath> --changed-between <old-ref> <new-ref> [--db <path>] [--verbose] [--dry-run] [--json] [--memory-trace] [--duration-format <auto|seconds|hms>] [--max-file-bytes <bytes>] [--include-symbol-kind <kind>[,<kind>]] [--exclude-symbol-kind <kind>[,<kind>]]"),
         ("index-files", "cdidx index <projectPath> --files <path> [path ...] [--db <path>] [--verbose] [--dry-run] [--json] [--memory-trace] [--duration-format <auto|seconds|hms>] [--max-file-bytes <bytes>] [--include-symbol-kind <kind>[,<kind>]] [--exclude-symbol-kind <kind>[,<kind>]]"),
-        ("search", "cdidx search <query>|--query <query>|-- <query>|--recipe <name|name/query>|--list-recipes|--named-query <name>=<query> [--named-query <name>=<query> ...] [--include-query <name>] [--exclude-query <name>] [--cursor <cursor>] [--audit-scope <source|all>] [--show-excluded] [--db <path>] [--json[=ndjson|array]] [--pretty] [--format <text|json|count|compact|csv|tsv|lsp|qf|sarif|issue-drafts>] [--open-issues <path|github|github:owner/name>] [--repo <owner/name>] [--issue-title <title>] [--issue-label <label>] [--verbose] [--limit <n>|--top <n>|--max-results <n>] [--lang <lang>] [--path <glob>] [--exclude-path <glob>] [--exclude-tests] [--exclude-comments] [--exclude-strings] [--exclude-fixtures] [--snippet-lines <n>] [--snippet-focus <leftmost|quality|proximity>] [--max-line-width <n>] [--fts] [--exact|--exact-substring] [--prefix] [--count] [--group-by <file|symbol>] [--since <datetime>] [--no-dedup] [--no-visibility-rank] [--require-before <query>] [--require-after <query>] [--reject-before <query>] [--reject-after <query>] [--guard-window <n>]"),
+        ("search", "cdidx search <query>|--query <query>|-- <query>|--recipe <name|name/query>|--list-recipes|--named-query <name>=<query> [--named-query <name>=<query> ...] [--include-query <name>] [--exclude-query <name>] [--cursor <cursor>] [--audit-scope <source|all>] [--show-excluded] [--db <path>] [--json[=ndjson|array]] [--pretty] [--format <text|json|count|compact|csv|tsv|lsp|qf|sarif|issue-drafts>] [--open-issues <path|github|github:owner/name>] [--repo <owner/name>] [--duplicate-confidence <low|medium|high>|--duplicate-threshold <score>] [--issue-title <title>] [--issue-label <label>] [--verbose] [--limit <n>|--top <n>|--max-results <n>] [--lang <lang>] [--path <glob>] [--exclude-path <glob>] [--exclude-tests] [--exclude-comments] [--exclude-strings] [--exclude-fixtures] [--snippet-lines <n>] [--snippet-focus <leftmost|quality|proximity>] [--max-line-width <n>] [--fts] [--exact|--exact-substring] [--prefix] [--count] [--group-by <file|symbol>] [--since <datetime>] [--no-dedup] [--no-visibility-rank] [--require-before <query>] [--require-after <query>] [--reject-before <query>] [--reject-after <query>] [--guard-window <n>]"),
         ("definition", "cdidx definition <query>|--query <query>|-- <query> [--db <path>] [--json] [--format <text|json|count|compact|csv|tsv|lsp|qf|sarif>] [--verbose] [--limit <n>|--top <n>] [--lang <lang>] [--kind <kind>] [--visibility <v[,v]>] [--exclude-visibility <v[,v]>] [--path <glob>] [--exclude-path <glob>] [--exclude-tests] [--body] [--exact|--exact-name] [--count] [--since <datetime>]"),
         ("goto", "cdidx goto <query>|--query <query>|-- <query> [--db <path>] [--json] [--limit <n>|--top <n>] [--lang <lang>] [--kind <kind>] [--path <glob>] [--exclude-path <glob>] [--exclude-tests] [--exact|--exact-name] [--all]"),
         ("references", "cdidx references <query>|--query <query>|-- <query> [--db <path>] [--json] [--format <text|json|count|compact|csv|tsv|lsp|qf|sarif>] [--verbose] [--limit <n>|--top <n>] [--lang <lang>] [--kind <kind>] [--path <glob>] [--exclude-path <glob>] [--exclude-tests] [--body] [--snippet-lines <n>] [--max-line-width <n>] [--exact|--exact-name] [--count]"),
@@ -114,7 +114,7 @@ private static readonly (string Command, string Usage)[] CommandUsageLines =
         ("deps", "cdidx deps [--db <path>] [--json] [--format <dot|graphml|json-graph|edgelist>] [--verbose] [--limit <n>|--top <n>] [--lang <lang>] [--path <glob>] [--exclude-path <glob>] [--exclude-tests] [--reverse] [--cycles]"),
         ("unused", "cdidx unused [--db <path>] [--json] [--compact] [--verbose] [--limit <n>|--top <n>] [--kind <kind>] [--bucket <bucket>] [--min-confidence <medium|low>] [--visibility <v[,v]>] [--exclude-visibility <v[,v]>] [--lang <lang>] [--path <glob>] [--exclude-path <glob>] [--exclude-tests] [--count] [--by-bucket]"),
         ("hotspots", "cdidx hotspots [--db <path>] [--json] [--verbose] [--limit <n>|--top <n>] [--kind <kind>] [--visibility <v[,v]>] [--exclude-visibility <v[,v]>] [--lang <lang>] [--path <glob>] [--exclude-path <glob>] [--exclude-tests] [--count] [--group-by <symbol|file|statement>] [--group-by-name]"),
-        ("suggestions", "cdidx suggestions <list|show|export> [id] [--db <path>] [--json] [--status <all|submitted|unsubmitted>] [--language <lang>] [--category <category>] [--since <datetime>] [--agent <name>] [--limit <n>] [--offset <n>] [--format <json|markdown|issue-drafts>] [--open-issues <path|github|github:owner/name>] [--repo <owner/name>]"),
+        ("suggestions", "cdidx suggestions <list|show|export> [id] [--db <path>] [--json] [--status <all|submitted|unsubmitted>] [--language <lang>] [--category <category>] [--since <datetime>] [--agent <name>] [--limit <n>] [--offset <n>] [--format <json|markdown|issue-drafts>] [--open-issues <path|github|github:owner/name>] [--repo <owner/name>] [--duplicate-confidence <low|medium|high>|--duplicate-threshold <score>]"),
         ("export", "cdidx export <archive> [--db <path>] [--json]"),
         ("export", "cdidx export ctags [--output <path>] [--db <path>] [--json] [--lang <lang>] [--path <glob>] [--exclude-path <glob>] [--exclude-tests]"),
         ("import", "cdidx import <archive> [--db <path>] [--prune-paths] [--dry-run|--check] [--json]"),

src/CodeIndex/Cli/IssueDuplicatePreflight.cs

@@ -18,6 +18,13 @@ internal sealed class IssueDuplicatePreflight
     internal const int MaxOpenIssueNumberLength = 32;
     internal const int MaxTitleTokenizationInputLength = MaxOpenIssueTitleLength;
     internal const int MaxGitHubRepositoryLength = 200;
+    internal const double LowDuplicateThreshold = 0.35;
+    internal const double DefaultDuplicateThreshold = 0.45;
+    internal const double HighDuplicateThreshold = 0.7;
+    internal const string LowDuplicateConfidence = "low";
+    internal const string DefaultDuplicateConfidence = "medium";
+    internal const string HighDuplicateConfidence = "high";
+    internal const string CustomDuplicateConfidence = "custom";
     private const int GitHubOpenIssuesPerPage = 100;
     private const int MaxGitHubOpenIssuePages = (MaxOpenIssueCount / GitHubOpenIssuesPerPage) + 1;
     private const string GitHubSourceName = "github";
@@ -129,7 +136,26 @@ public static bool TryLoad(string? source, string? repository, out IssueDuplicat
         return TryLoadFromGitHub(normalizedRepository, out preflight, out error);
     }
 
+    public static bool TryNormalizeDuplicateConfidence(string value, out string confidence)
+    {
+        confidence = value.Trim().ToLowerInvariant();
+        return confidence is LowDuplicateConfidence or DefaultDuplicateConfidence or HighDuplicateConfidence;
+    }
+
+    public static double ThresholdForDuplicateConfidence(string confidence) => confidence switch
+    {
+        LowDuplicateConfidence => LowDuplicateThreshold,
+        HighDuplicateConfidence => HighDuplicateThreshold,
+        _ => DefaultDuplicateThreshold,
+    };
+
     public List<SuggestionIssueDraftDuplicateMatchJsonResult> FindMatches(string draftTitle, IReadOnlyList<string> draftLabels)
+        => FindMatches(draftTitle, draftLabels, DefaultDuplicateThreshold);
+
+    public List<SuggestionIssueDraftDuplicateMatchJsonResult> FindMatches(
+        string draftTitle,
+        IReadOnlyList<string> draftLabels,
+        double minimumScore)
     {
         if (!Checked || _issues.Count == 0)
             return [];
@@ -153,13 +179,14 @@ public List<SuggestionIssueDraftDuplicateMatchJsonResult> FindMatches(string dra
             string? reason = null;
             if (normalizedIssueTitle.Length > 0 && normalizedIssueTitle == normalizedDraftTitle)
             {
-                reason = "title_exact";
                 score = 1.0;
+                if (score >= minimumScore)
+                    reason = "title_exact";
             }
             else if (overlappingLabels.Count > 0)
             {
                 score = ScoreTitleSimilarity(draftTokens, TokenizeTitle(issue.Title));
-                if (score >= 0.45)
+                if (score >= minimumScore)
                 {
                     reason = "title_label_similarity";
                 }
@@ -168,8 +195,9 @@ public List<SuggestionIssueDraftDuplicateMatchJsonResult> FindMatches(string dra
                     && (normalizedIssueTitle.Contains(normalizedDraftTitle, StringComparison.Ordinal)
                         || normalizedDraftTitle.Contains(normalizedIssueTitle, StringComparison.Ordinal)))
                 {
-                    reason = "title_label_contains";
-                    score = Math.Max(score, 0.45);
+                    score = Math.Max(score, DefaultDuplicateThreshold);
+                    if (score >= minimumScore)
+                        reason = "title_label_contains";
                 }
             }
 

src/CodeIndex/Cli/JsonOutputContracts.cs

@@ -605,6 +605,7 @@ internal sealed record VersionInfoJsonResult(
 [JsonSerializable(typeof(SearchIssueDraftExportJsonResult))]
 [JsonSerializable(typeof(SearchIssueDraftJsonResult))]
 [JsonSerializable(typeof(SearchIssueDraftSourceJsonResult))]
+[JsonSerializable(typeof(IssueDraftTriageMetadataJsonResult))]
 [JsonSerializable(typeof(SearchNextMatchHint))]
 [JsonSerializable(typeof(SearchResult))]
 [JsonSerializable(typeof(SearchTermOccurrence))]