fix: resolve .gomuignore and Not Viable mutation issues

.github/workflows/mutation-testing.yml

@@ -35,6 +35,6 @@ jobs:
         version: 'local'
         workers: '2'
         timeout: '60'
-        threshold: 0
-        fail-on-gate: 'false'  # TODO: Fix gomu bugs (.gomuignore, incremental analysis, not viable rate)
+        threshold: '40'  # Current baseline ~46%, will improve incrementally
+        fail-on-gate: 'true'
 

internal/analysis/git.go

@@ -67,11 +67,16 @@ func (g *GitIntegration) GetChangedFiles(baseBranch string) ([]string, error) {
 		return []string{}, nil
 	}
 
-	// Filter for Go files
+	// Filter for Go files and apply ignore patterns
 	var goFiles []string
 
 	for _, file := range files {
 		if IsGoSourceFile(file) {
+			// Check if file should be ignored by .gomuignore
+			if g.ignoreParser != nil && g.ignoreParser.ShouldIgnore(file) {
+				continue
+			}
+
 			// Convert to absolute path
 			absPath := filepath.Join(g.workDir, file)
 			goFiles = append(goFiles, absPath)

internal/analysis/incremental.go

@@ -25,6 +25,7 @@ type IncrementalAnalyzer struct {
 	history      HistoryStore
 	workDir      string
 	ignoreParser IgnoreParser
+	incremental  bool
 }
 
 // IgnoreParser defines the interface for ignore file parsing.
@@ -33,7 +34,7 @@ type IgnoreParser interface {
 }
 
 // NewIncrementalAnalyzer creates a new incremental analyzer.
-func NewIncrementalAnalyzer(workDir string, historyStore HistoryStore) (*IncrementalAnalyzer, error) {
+func NewIncrementalAnalyzer(workDir string, historyStore HistoryStore, incremental bool) (*IncrementalAnalyzer, error) {
 	// Validate that the workDir exists
 	if _, err := os.Stat(workDir); err != nil {
 		if os.IsNotExist(err) {
@@ -44,10 +45,11 @@ func NewIncrementalAnalyzer(workDir string, historyStore HistoryStore) (*Increme
 	}
 
 	return &IncrementalAnalyzer{
-		hasher:  NewFileHasher(),
-		git:     NewGitIntegration(workDir),
-		history: historyStore,
-		workDir: workDir,
+		hasher:      NewFileHasher(),
+		git:         NewGitIntegration(workDir),
+		history:     historyStore,
+		workDir:     workDir,
+		incremental: incremental,
 	}, nil
 }
 
@@ -91,9 +93,7 @@ func (a *IncrementalAnalyzer) AnalyzeFiles() ([]FileAnalysisResult, error) {
 
 // getFilesToAnalyze returns the list of files that should be analyzed.
 func (a *IncrementalAnalyzer) getFilesToAnalyze() ([]string, error) {
-	// Always enable incremental analysis by default
-	incrementalEnabled := true
-	if incrementalEnabled && a.git.IsGitRepository() {
+	if a.incremental && a.git.IsGitRepository() {
 		// Use Git diff to get changed files with intelligent default base branch
 		return a.git.GetChangedFiles("main")
 	}

internal/analysis/incremental_test.go

@@ -49,7 +49,7 @@ func TestIncrementalAnalyzer_NewIncrementalAnalyzer(t *testing.T) {
 	tempDir := t.TempDir()
 	history := NewMockHistoryStore()
 
-	analyzer, err := NewIncrementalAnalyzer(tempDir, history)
+	analyzer, err := NewIncrementalAnalyzer(tempDir, history, false)
 	if err != nil {
 		t.Fatalf("Failed to create incremental analyzer: %v", err)
 	}
@@ -86,7 +86,7 @@ func TestIncrementalAnalyzer_AnalyzeFiles(t *testing.T) {
 		t.Fatalf("Failed to create go.mod: %v", err)
 	}
 
-	analyzer, err := NewIncrementalAnalyzer(tempDir, history)
+	analyzer, err := NewIncrementalAnalyzer(tempDir, history, false)
 	if err != nil {
 		t.Fatalf("Failed to create incremental analyzer: %v", err)
 	}
@@ -142,7 +142,7 @@ func TestIncrementalAnalyzer_GetFilesNeedingUpdate(t *testing.T) {
 		t.Fatalf("Failed to create go.mod: %v", err)
 	}
 
-	analyzer, err := NewIncrementalAnalyzer(tempDir, history)
+	analyzer, err := NewIncrementalAnalyzer(tempDir, history, false)
 	if err != nil {
 		t.Fatalf("Failed to create incremental analyzer: %v", err)
 	}
@@ -187,7 +187,7 @@ func TestIncrementalAnalyzer_PrintAnalysisReport(t *testing.T) {
 	history := NewMockHistoryStore()
 	tempDir := t.TempDir()
 
-	analyzer, err := NewIncrementalAnalyzer(tempDir, history)
+	analyzer, err := NewIncrementalAnalyzer(tempDir, history, false)
 	if err != nil {
 		t.Fatalf("Failed to create incremental analyzer: %v", err)
 	}
@@ -218,7 +218,7 @@ func TestIncrementalAnalyzer_EdgeCases(t *testing.T) {
 	history := NewMockHistoryStore()
 
 	// Test with empty directory
-	analyzer, err := NewIncrementalAnalyzer(tempDir, history)
+	analyzer, err := NewIncrementalAnalyzer(tempDir, history, false)
 	if err != nil {
 		t.Fatalf("Failed to create incremental analyzer: %v", err)
 	}
@@ -247,7 +247,7 @@ func TestIncrementalAnalyzer_InvalidPath(t *testing.T) {
 	history := NewMockHistoryStore()
 
 	// Test with non-existent directory
-	_, err := NewIncrementalAnalyzer("/nonexistent/path", history)
+	_, err := NewIncrementalAnalyzer("/nonexistent/path", history, false)
 	if err == nil {
 		t.Error("Expected error for non-existent path")
 	}
@@ -259,7 +259,7 @@ func TestIncrementalAnalyzer_analyzeFile(t *testing.T) {
 
 	mockHistory := NewMockHistoryStore()
 
-	analyzer, err := NewIncrementalAnalyzer(tmpDir, mockHistory)
+	analyzer, err := NewIncrementalAnalyzer(tmpDir, mockHistory, false)
 	if err != nil {
 		t.Fatalf("Failed to create incremental analyzer: %v", err)
 	}
@@ -346,7 +346,7 @@ func TestIncrementalAnalyzer_hasTestFilesChanged(t *testing.T) {
 	tmpDir := t.TempDir()
 	mockHistory := NewMockHistoryStore()
 
-	analyzer, err := NewIncrementalAnalyzer(tmpDir, mockHistory)
+	analyzer, err := NewIncrementalAnalyzer(tmpDir, mockHistory, false)
 	if err != nil {
 		t.Fatalf("Failed to create incremental analyzer: %v", err)
 	}

internal/execution/engine.go

@@ -132,8 +132,8 @@ func (e *Engine) checkCompilationWithOverlay(mutCtx *MutationContext) error {
 	// Get the directory containing the original file for compilation
 	compileDir := filepath.Dir(mutCtx.OriginalPath)
 
-	// Build only the specific file to avoid issues with other invalid files in the directory
-	cmd := exec.CommandContext(ctx, "go", "build", "-overlay="+mutCtx.OverlayPath, filepath.Base(mutCtx.OriginalPath))
+	// Build the entire package with overlay to properly resolve dependencies
+	cmd := exec.CommandContext(ctx, "go", "build", "-overlay="+mutCtx.OverlayPath, ".")
 	cmd.Dir = compileDir
 
 	output, err := cmd.CombinedOutput()

pkg/gomu/engine.go

@@ -187,7 +187,7 @@ func (e *Engine) performIncrementalAnalysis(absPath string, opts *RunOptions, ig
 
 	var err error
 
-	e.incrementalAnalyzer, err = analysis.NewIncrementalAnalyzer(absPath, historyWrapper)
+	e.incrementalAnalyzer, err = analysis.NewIncrementalAnalyzer(absPath, historyWrapper, opts.Incremental)
 	if err != nil {
 		return nil, nil, fmt.Errorf("failed to create incremental analyzer: %w", err)
 	}