Resolve indexed roots for project filters and LSP output

changelog.d/unreleased/3151.fixed.md

@@ -0,0 +1,16 @@
+---
+category: fixed
+issues:
+  - 3151
+affected:
+  - src/CodeIndex/Cli/QueryCommandRunner.cs
+  - tests/CodeIndex.Tests/QueryCommandRunnerTests.cs
+---
+
+## English
+
+- **CLI LSP locations now resolve indexed relative paths from the indexed project root (#3151)** - `--format lsp` now builds file URIs from the active indexed project root when indexed paths are relative, falling back to the current directory only when no indexed root is available.
+
+## 日本語
+
+- **CLI LSP location が indexed relative path を indexed project root から解決するようになりました (#3151)** - `--format lsp` は indexed path が相対パスの場合に active な indexed project root から file URI を構築し、indexed root が利用できない場合だけ current directory にフォールバックします。

changelog.d/unreleased/3183.fixed.md

@@ -0,0 +1,16 @@
+---
+category: fixed
+issues:
+  - 3183
+affected:
+  - src/CodeIndex/Mcp/McpToolHandlers.cs
+  - tests/CodeIndex.Tests/McpServerTests.cs
+---
+
+## English
+
+- **MCP project filters now resolve against the indexed project root (#3183)** - MCP tools that accept `project` now expand solution project filters from the database's active indexed project root instead of the server process current directory.
+
+## 日本語
+
+- **MCP の project filter が indexed project root 基準で解決されるようになりました (#3183)** - `project` を受け取る MCP tool は server process の current directory ではなく、database の active indexed project root から solution project filter を展開します。

changelog.d/unreleased/3189.fixed.md

@@ -0,0 +1,16 @@
+---
+category: fixed
+issues:
+  - 3189
+affected:
+  - src/CodeIndex/Cli/QueryCommandRunner.cs
+  - tests/CodeIndex.Tests/QueryCommandRunnerTests.cs
+---
+
+## English
+
+- **CLI project filters now resolve against the indexed project root (#3189)** - query commands with `--project` now expand solution project filters from the active indexed project root, so explicit `--db` queries launched from another current directory do not inspect the wrong workspace.
+
+## 日本語
+
+- **CLI の project filter が indexed project root 基準で解決されるようになりました (#3189)** - `--project` 付き query コマンドは active な indexed project root から solution project filter を展開するため、別の current directory から明示 `--db` query を実行しても誤った workspace を参照しません。

src/CodeIndex/Cli/QueryCommandRunner.cs

@@ -44,6 +44,12 @@ public static class QueryCommandRunner
 
     [ThreadStatic]
     private static DbReader? s_batchReader;
+    [ThreadStatic]
+    private static string? s_batchDbPath;
+    [ThreadStatic]
+    private static bool s_batchDbPathExplicit;
+    [ThreadStatic]
+    private static string? s_activeQueryProjectRoot;
 
     private static DateTime GetUtcNow() => TimeProvider.GetUtcNow().UtcDateTime;
 
@@ -268,6 +274,7 @@ private sealed record StatusReadinessField(
     public static int RunBatch(string[] cmdArgs, JsonSerializerOptions jsonOptions)
     {
         var dbPath = Path.Combine(".cdidx", "codeindex.db");
+        var dbPathExplicit = false;
         for (var i = 0; i < cmdArgs.Length; i++)
         {
             var arg = cmdArgs[i];
@@ -279,6 +286,7 @@ public static int RunBatch(string[] cmdArgs, JsonSerializerOptions jsonOptions)
                     return CommandExitCodes.UsageError;
                 }
                 dbPath = cmdArgs[++i];
+                dbPathExplicit = true;
                 continue;
             }
 
@@ -290,6 +298,7 @@ public static int RunBatch(string[] cmdArgs, JsonSerializerOptions jsonOptions)
                     Console.Error.WriteLine(BuildMissingOptionValueError("--db"));
                     return CommandExitCodes.UsageError;
                 }
+                dbPathExplicit = true;
                 continue;
             }
 
@@ -314,6 +323,8 @@ public static int RunBatch(string[] cmdArgs, JsonSerializerOptions jsonOptions)
 
             db.TryMigrateForRead();
             s_batchReader = new DbReader(db);
+            s_batchDbPath = dbPath;
+            s_batchDbPathExplicit = dbPathExplicit;
             var firstFailure = CommandExitCodes.Success;
             var lineNumber = 0;
             while (TryReadBatchLine(Console.In, out var line, out var lineExceededLimit))
@@ -347,6 +358,8 @@ public static int RunBatch(string[] cmdArgs, JsonSerializerOptions jsonOptions)
         finally
         {
             s_batchReader = null;
+            s_batchDbPath = null;
+            s_batchDbPathExplicit = false;
         }
     }
 
@@ -1147,11 +1160,14 @@ public static void AttachLspLocations(IEnumerable<ReferenceResult> results)
         }
     }
 
-    public static LspLocation BuildLspLocation(string path, int startLine, int startColumn, int endLine, int endColumn)
+    public static LspLocation BuildLspLocation(string path, int startLine, int startColumn, int endLine, int endColumn, string? projectRoot = null)
     {
+        var baseRoot = string.IsNullOrWhiteSpace(projectRoot)
+            ? s_activeQueryProjectRoot ?? Environment.CurrentDirectory
+            : projectRoot;
         var absolutePath = Path.IsPathFullyQualified(path)
             ? path
-            : Path.GetFullPath(path, Environment.CurrentDirectory);
+            : Path.GetFullPath(path, baseRoot);
         return new LspLocation
         {
             Uri = new Uri(absolutePath).AbsoluteUri,
@@ -6736,11 +6752,15 @@ void WarnIfDuplicateSingleValueOption(string canonicalName, string newValue)
             }
         }
 
+        var dbResolution = DbPathResolver.ResolveForQuery(Environment.CurrentDirectory, dbPath, dataDir);
+        var resolvedDbPath = dbResolution.DbPath;
+
         if (parseErrors == null && projectFilters.Count > 0)
         {
             try
             {
-                foreach (var glob in SolutionProjectResolver.ResolveProjectDirectoryGlobs(Environment.CurrentDirectory, projectFilters, solutionFilter))
+                var projectRoot = ResolveProjectFilterRoot(resolvedDbPath, dbPathExplicit);
+                foreach (var glob in SolutionProjectResolver.ResolveProjectDirectoryGlobs(projectRoot, projectFilters, solutionFilter))
                     pathPatterns.Add(glob);
             }
             catch (Exception ex) when (ex is IOException or UnauthorizedAccessException or InvalidOperationException)
@@ -6760,8 +6780,6 @@ void WarnIfDuplicateSingleValueOption(string canonicalName, string newValue)
         if (validateDefaultMaxLineWidth && !maxLineWidthExplicit && defaultMaxLineWidthError != null)
             AddParseError(defaultMaxLineWidthError);
 
-        var dbResolution = DbPathResolver.ResolveForQuery(Environment.CurrentDirectory, dbPath, dataDir);
-        var resolvedDbPath = dbResolution.DbPath;
         if (readOnly)
         {
             var canAppendReadOnlyFlags = !SqliteFileUri.StartsWithFileScheme(resolvedDbPath) ||
@@ -6853,6 +6871,18 @@ void WarnIfDuplicateSingleValueOption(string canonicalName, string newValue)
         };
     }
 
+    private static string ResolveProjectFilterRoot(string dbPath, bool dbPathExplicit)
+    {
+        var effectiveDbPath = s_batchReader != null && !string.IsNullOrWhiteSpace(s_batchDbPath)
+            ? s_batchDbPath!
+            : dbPath;
+        var effectiveDbPathExplicit = s_batchReader != null && !string.IsNullOrWhiteSpace(s_batchDbPath)
+            ? s_batchDbPathExplicit
+            : dbPathExplicit;
+        return DbPathResolver.ResolveProjectRootForQuery(effectiveDbPath, effectiveDbPathExplicit)
+            ?? Environment.CurrentDirectory;
+    }
+
     private static List<string> ParseMapSections(string rawValue, Action<string> addParseError)
     {
         var sections = new List<string>();
@@ -7416,7 +7446,17 @@ private static int WithDb(QueryCommandOptions options, JsonSerializerOptions jso
             }
 
             reader.IncludeGenerated = options.IncludeGenerated;
-            var exitCode = reader.RunWithGeneratedScope(() => action(reader));
+            var previousProjectRoot = s_activeQueryProjectRoot;
+            s_activeQueryProjectRoot = ResolveProjectFilterRoot(dbPath, options.DbPathExplicit);
+            int exitCode;
+            try
+            {
+                exitCode = reader.RunWithGeneratedScope(() => action(reader));
+            }
+            finally
+            {
+                s_activeQueryProjectRoot = previousProjectRoot;
+            }
             var profileEntries = profiling ? Database.DbDebug.EndProfile() : [];
             if (options.Profile)
                 WriteProfilePayload(profileEntries, jsonOptions);

src/CodeIndex/Mcp/McpToolHandlers.cs

@@ -1014,20 +1014,21 @@ private JsonObject ToAnalyzeSymbolJsonObject(SymbolAnalysisResult analysis)
         return string.IsNullOrWhiteSpace(value) ? null : new List<string> { value };
     }
 
-    private static List<string>? ReadScopedPathList(JsonNode? args)
+    private List<string>? ReadScopedPathList(JsonNode? args)
     {
         var paths = ReadPathList(args, "path") ?? [];
         var projects = ReadPathList(args, "project") ?? [];
         if (projects.Count == 0)
             return paths.Count == 0 ? null : paths;
 
         var solution = args?["solution"]?.GetValue<string>();
-        foreach (var glob in SolutionProjectResolver.ResolveProjectDirectoryGlobs(Environment.CurrentDirectory, projects, solution))
+        var projectRoot = ResolveProjectFilterRoot();
+        foreach (var glob in SolutionProjectResolver.ResolveProjectDirectoryGlobs(projectRoot, projects, solution))
             paths.Add(glob);
         return paths.Count == 0 ? null : paths;
     }
 
-    private static JsonObject? ValidateProjectFilterArguments(JsonNode? args)
+    private JsonObject? ValidateProjectFilterArguments(JsonNode? args)
     {
         var projects = ReadPathList(args, "project") ?? [];
         if (projects.Count == 0)
@@ -1036,7 +1037,7 @@ private JsonObject ToAnalyzeSymbolJsonObject(SymbolAnalysisResult analysis)
         var solution = args?["solution"]?.GetValue<string>();
         try
         {
-            _ = SolutionProjectResolver.ResolveProjectDirectoryGlobs(Environment.CurrentDirectory, projects, solution);
+            _ = SolutionProjectResolver.ResolveProjectDirectoryGlobs(ResolveProjectFilterRoot(), projects, solution);
             return null;
         }
         catch (Exception ex) when (ex is IOException or UnauthorizedAccessException or InvalidOperationException)
@@ -1053,6 +1054,10 @@ private JsonObject ToAnalyzeSymbolJsonObject(SymbolAnalysisResult analysis)
         }
     }
 
+    private string ResolveProjectFilterRoot()
+        => DbPathResolver.ResolveProjectRootForQuery(_dbPath, _dbPathExplicit)
+            ?? Environment.CurrentDirectory;
+
     private static bool TryReadSinceArgument(JsonNode? args, out DateTime? since, out string? error)
     {
         var sinceStr = args?["since"]?.GetValue<string>();

tests/CodeIndex.Tests/McpServerTests.cs

@@ -9999,6 +9999,48 @@ public void Call(ServiceB service)
         }
     }
 
+    [Fact]
+    public void ToolsCall_ProjectScopeUsesIndexedProjectRootWhenCurrentDirectoryDiffers_Issue3183()
+    {
+        var projectRoot = TestProjectHelper.CreateTempProject("cdidx_mcp_project_scope_indexed_root");
+        var otherRoot = TestProjectHelper.CreateTempProject("cdidx_mcp_project_scope_other_cwd");
+        var originalCurrentDirectory = Environment.CurrentDirectory;
+        try
+        {
+            Directory.CreateDirectory(Path.Combine(projectRoot, "src", "AppA"));
+            Directory.CreateDirectory(Path.Combine(projectRoot, "src", "AppB"));
+            File.WriteAllText(Path.Combine(projectRoot, "Repo.sln"), """
+            Microsoft Visual Studio Solution File, Format Version 12.00
+            Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "AppA", "src\AppA\AppA.csproj", "{11111111-1111-1111-1111-111111111111}"
+            EndProject
+            Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "AppB", "src\AppB\AppB.csproj", "{22222222-2222-2222-2222-222222222222}"
+            EndProject
+            """);
+            File.WriteAllText(Path.Combine(projectRoot, "src", "AppA", "AppA.csproj"), "<Project Sdk=\"Microsoft.NET.Sdk\" />");
+            File.WriteAllText(Path.Combine(projectRoot, "src", "AppB", "AppB.csproj"), "<Project Sdk=\"Microsoft.NET.Sdk\" />");
+
+            var dbPath = TestProjectHelper.CreateProjectDb(projectRoot);
+            TestProjectHelper.InsertIndexedFile(dbPath, "src/AppA/ServiceA.cs", "csharp", "public class ServiceA { }\n");
+            TestProjectHelper.InsertIndexedFile(dbPath, "src/AppB/ServiceB.cs", "csharp", "public class ServiceB { }\n");
+
+            Environment.CurrentDirectory = otherRoot;
+            using var server = new McpServer(dbPath, ConsoleUi.LoadVersion(), dbPathExplicit: true);
+            var request = JsonNode.Parse("""{"jsonrpc":"2.0","id":1,"method":"tools/call","params":{"name":"search","arguments":{"query":"Service","project":"AppA","exactSubstring":true}}}""")!;
+            var response = server.HandleMessage(request)!;
+
+            Assert.False(response["result"]!["isError"]?.GetValue<bool>() ?? false);
+            var results = response["result"]!["structuredContent"]!["results"]!.AsArray();
+            var result = Assert.Single(results);
+            Assert.Equal("src/AppA/ServiceA.cs", result!["path"]!.GetValue<string>());
+        }
+        finally
+        {
+            Environment.CurrentDirectory = originalCurrentDirectory;
+            TestProjectHelper.DeleteDirectory(otherRoot);
+            TestProjectHelper.DeleteDirectory(projectRoot);
+        }
+    }
+
     [Fact]
     public void ToolsCall_Index_Rebuild_IgnoresUnreadableDirectoriesWhenCollectingMarkerFingerprints()
     {

tests/CodeIndex.Tests/QueryCommandRunnerTests.cs

@@ -299,6 +299,82 @@ public void ParseArgs_ProjectFilterExpandsSolutionProjectToPathGlob_Issue1707()
         }
     }
 
+    [Fact]
+    public void ParseArgs_ProjectFilterUsesIndexedProjectRootForExplicitDb_Issue3189()
+    {
+        var projectRoot = TestProjectHelper.CreateTempProject("cdidx_solution_filter_explicit_db");
+        var otherRoot = TestProjectHelper.CreateTempProject("cdidx_solution_filter_other_cwd");
+        var originalCurrentDirectory = Environment.CurrentDirectory;
+        try
+        {
+            Directory.CreateDirectory(Path.Combine(projectRoot, "src", "App"));
+            File.WriteAllText(Path.Combine(projectRoot, "CodeIndex.sln"), """
+            Microsoft Visual Studio Solution File, Format Version 12.00
+            Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "App", "src\App\App.csproj", "{11111111-1111-1111-1111-111111111111}"
+            EndProject
+            """);
+            File.WriteAllText(Path.Combine(projectRoot, "src", "App", "App.csproj"), "<Project Sdk=\"Microsoft.NET.Sdk\" />");
+            var dbPath = TestProjectHelper.CreateProjectDb(projectRoot);
+
+            Environment.CurrentDirectory = otherRoot;
+            var options = QueryCommandRunner.ParseArgs(
+                ["Auth", "--db", dbPath, "--project", "App"],
+                jsonDefault: false,
+                allowNamedQuery: true);
+
+            Assert.Equal("Auth", options.Query);
+            Assert.Equal(["App"], options.ProjectFilters);
+            Assert.Equal(["src/App/*"], options.PathPatterns);
+            Assert.Null(options.ParseError);
+        }
+        finally
+        {
+            Environment.CurrentDirectory = originalCurrentDirectory;
+            TestProjectHelper.DeleteDirectory(otherRoot);
+            TestProjectHelper.DeleteDirectory(projectRoot);
+        }
+    }
+
+    [Fact]
+    public void RunDefinition_LspFormatUsesIndexedProjectRootForExplicitDb_Issue3151()
+    {
+        var projectRoot = TestProjectHelper.CreateTempProject("cdidx_lsp_explicit_db_root");
+        var otherRoot = TestProjectHelper.CreateTempProject("cdidx_lsp_other_cwd");
+        var originalCurrentDirectory = Environment.CurrentDirectory;
+        try
+        {
+            var dbPath = TestProjectHelper.CreateProjectDb(projectRoot);
+            TestProjectHelper.InsertIndexedFile(
+                dbPath,
+                "src/App/Service.cs",
+                "csharp",
+                """
+                public class Service
+                {
+                    public void Run() { }
+                }
+                """);
+
+            Environment.CurrentDirectory = otherRoot;
+            var (exitCode, stdout, stderr) = CaptureConsole(() => QueryCommandRunner.RunDefinition(
+                ["Service", "--db", dbPath, "--format", "lsp", "--exact-name", "--lang", "csharp", "--kind", "class"],
+                _jsonOptions));
+
+            Assert.Equal(CommandExitCodes.Success, exitCode);
+            Assert.Equal(string.Empty, stderr);
+            using var document = JsonDocument.Parse(stdout);
+            var location = Assert.Single(document.RootElement.EnumerateArray());
+            var expectedUri = new Uri(Path.Combine(projectRoot, "src", "App", "Service.cs")).AbsoluteUri;
+            Assert.Equal(expectedUri, location.GetProperty("uri").GetString());
+        }
+        finally
+        {
+            Environment.CurrentDirectory = originalCurrentDirectory;
+            TestProjectHelper.DeleteDirectory(otherRoot);
+            TestProjectHelper.DeleteDirectory(projectRoot);
+        }
+    }
+
     [Theory]
     [InlineData("30m", 30 * 60)]
     [InlineData("2h", 2 * 60 * 60)]