Fix relative CLI paths for config and file options

Resolve config paths with Path.GetFullPath before SetBasePath, and normalize baseline, output, and coverage paths in AnalysisWorkflow.Prepare.

Co-authored-by: Cursor <cursoragent@cursor.com>

Author: floriankraemer

CognitiveCodeAnalysis.Tests/src/Application/AnalysisWorkflowTests.cs

@@ -30,7 +30,7 @@ public void Prepare_ResolvesPathsAndDefaults()
 
         Assert.That(prepared.AbsoluteSourcePath, Is.EqualTo(Path.GetFullPath(".")));
         Assert.That(prepared.ReportType, Is.EqualTo("Html"));
-        Assert.That(prepared.OutputFile, Is.EqualTo("cognitive-analysis-report"));
+        Assert.That(prepared.OutputFile, Is.EqualTo(Path.GetFullPath("cognitive-analysis-report")));
         Assert.That(prepared.IsConsoleTextReport, Is.False);
     }
 
@@ -49,7 +49,28 @@ public void Prepare_RecognizesConsoleTextReport()
         ));
 
         Assert.That(prepared.IsConsoleTextReport, Is.True);
-        Assert.That(prepared.OutputFile, Is.EqualTo("out.txt"));
+        Assert.That(prepared.OutputFile, Is.EqualTo(Path.GetFullPath("out.txt")));
+    }
+
+    [Test]
+    public void Prepare_ResolvesRelativeBaselineAndOutputPaths()
+    {
+        var workflow = CreateWorkflow();
+        var baseline = Path.Combine(".", "baseline.json");
+        var output = Path.Combine(".", "report.html");
+
+        var prepared = workflow.Prepare(new AnalysisRequest(
+            SourcePath: ".",
+            ConfigFile: null,
+            ReportType: "Html",
+            BaselineFile: baseline,
+            OutputFile: output,
+            CoverageCobertura: Path.Combine(".", "coverage.xml")
+        ));
+
+        Assert.That(prepared.BaselineFile, Is.EqualTo(Path.GetFullPath(baseline)));
+        Assert.That(prepared.OutputFile, Is.EqualTo(Path.GetFullPath(output)));
+        Assert.That(prepared.CoverageCobertura, Is.EqualTo(Path.GetFullPath(Path.Combine(".", "coverage.xml"))));
     }
 
     [Test]

CognitiveCodeAnalysis.Tests/src/Configuration/ConfigurationLoaderTests.cs

@@ -98,6 +98,42 @@ public void ConfigureServices_GetConfiguration_RoundTrips()
         }
     }
 
+    [Test]
+    public void Load_RelativeConfigPath_ResolvesAgainstCurrentDirectory()
+    {
+        var json = """
+            {
+              "cognitive": {
+                "scoreThreshold": 3.21
+              }
+            }
+            """;
+        var dir = Path.Combine(Path.GetTempPath(), "cogcfg-rel-" + Guid.NewGuid());
+        var subDir = Path.Combine(dir, "config");
+        Directory.CreateDirectory(subDir);
+        var file = Path.Combine(subDir, "custom.json");
+        var originalCwd = Directory.GetCurrentDirectory();
+        try
+        {
+            File.WriteAllText(file, json);
+            Directory.SetCurrentDirectory(dir);
+            var cfg = ConfigurationLoader.Load(Path.Combine("config", "custom.json"));
+            Assert.That(cfg.ScoreThreshold, Is.EqualTo(3.21));
+        }
+        finally
+        {
+            Directory.SetCurrentDirectory(originalCwd);
+            try
+            {
+                Directory.Delete(dir, recursive: true);
+            }
+            catch
+            {
+                // ignore
+            }
+        }
+    }
+
     [Test]
     public void Load_WithoutConfigFile_UsesBundledDefaults()
     {

CognitiveCodeAnalysis/src/Application/AnalysisWorkflow.cs

@@ -1,4 +1,4 @@
-/// <copyright company="Florian Krämer">
+/// <copyright company="Florian Krämer">
 ///     Licensed under the MIT license. See LICENSE file in the project root for full license information.
 /// </copyright>
 
@@ -20,20 +20,23 @@ public PreparedAnalysis Prepare(AnalysisRequest request)
         var sourcePath = request.SourcePath ?? Directory.GetCurrentDirectory();
         var absoluteSourcePath = Path.GetFullPath(sourcePath);
         var reportType = request.ReportType;
-        var outputFile = request.OutputFile ?? "cognitive-analysis-report";
+        var outputFile = Path.GetFullPath(request.OutputFile ?? "cognitive-analysis-report");
         var isConsoleTextReport = string.Equals(reportType, "ConsoleText", StringComparison.OrdinalIgnoreCase);
 
         return new PreparedAnalysis(
             Configuration: configuration,
             AbsoluteSourcePath: absoluteSourcePath,
             ReportType: reportType,
             OutputFile: outputFile,
-            BaselineFile: request.BaselineFile,
-            CoverageCobertura: request.CoverageCobertura,
+            BaselineFile: ToAbsolutePath(request.BaselineFile),
+            CoverageCobertura: ToAbsolutePath(request.CoverageCobertura),
             IsConsoleTextReport: isConsoleTextReport
         );
     }
 
+    private static string? ToAbsolutePath(string? path) =>
+        string.IsNullOrWhiteSpace(path) ? path : Path.GetFullPath(path);
+
     public List<string> FindSourceFiles(string absoluteSourcePath, IProgress<AnalysisProgress>? progress = null)
         => cognitiveAnalysisFacade.FindSourceFiles(absoluteSourcePath, progress);
 

CognitiveCodeAnalysis/src/Configuration/ConfigurationLoader.cs

@@ -66,9 +66,9 @@ private static IConfigurationRoot BuildConfiguration(string? configFilePath = nu
 
         if (string.IsNullOrEmpty(configFilePath)) return GetDefaultConfig();
 
-        // If a specific file path is provided, use it directly
-        string directory = Path.GetDirectoryName(configFilePath) ?? AppContext.BaseDirectory;
-        string fileName = Path.GetFileName(configFilePath);
+        string fullConfigPath = Path.GetFullPath(configFilePath);
+        string directory = Path.GetDirectoryName(fullConfigPath) ?? AppContext.BaseDirectory;
+        string fileName = Path.GetFileName(fullConfigPath);
 
         return builder.SetBasePath(directory)
                 .AddJsonFile(fileName, optional: false, reloadOnChange: false)