diff --git a/.gptinclude b/.gptinclude
index 8431972..0d5ea5a 100644
--- a/.gptinclude
+++ b/.gptinclude
@@ -1 +1 @@
-prompt/
\ No newline at end of file
+prompt
diff --git a/prompt/pattern_fix_test.go b/prompt/pattern_fix_test.go
new file mode 100644
index 0000000..be1bd5a
--- /dev/null
+++ b/prompt/pattern_fix_test.go
@@ -0,0 +1,145 @@
+package prompt
+
+import (
+	"os"
+	"path/filepath"
+	"testing"
+)
+
+func TestExtensionPatternFix(t *testing.T) {
+	// Create a temporary directory structure for testing
+	tempDir, err := os.MkdirTemp("", "git2gpt-pattern-test")
+	if err != nil {
+		t.Fatalf("Failed to create temp directory: %v", err)
+	}
+	defer os.RemoveAll(tempDir)
+
+	// Create test files
+	testFiles := []struct {
+		path     string
+		contents string
+	}{
+		{"file.go", "package main"},                    // Root level .go file
+		{"config.json", `{"test": true}`},              // Root level .json file
+		{"README.md", "# Root readme"},                 // Root level .md file
+		{"src/main.go", "package main\nfunc main(){}"},// Nested .go file
+		{"src/config.json", `{"nested": true}`},        // Nested .json file
+		{"docs/api.md", "# API docs"},                  // Nested .md file
+		{"deep/nested/file.go", "package deep"},        // Deeply nested .go file
+	}
+
+	for _, tf := range testFiles {
+		fullPath := filepath.Join(tempDir, tf.path)
+		dir := filepath.Dir(fullPath)
+		if err := os.MkdirAll(dir, 0755); err != nil {
+			t.Fatalf("Failed to create directory %s: %v", dir, err)
+		}
+		if err := os.WriteFile(fullPath, []byte(tf.contents), 0644); err != nil {
+			t.Fatalf("Failed to write file %s: %v", fullPath, err)
+		}
+	}
+
+	// Test case: Include all .md files (both root and nested), ignore all .go files (both root and nested)
+	t.Run("Extension patterns should match both root and nested files", func(t *testing.T) {
+		// Create .gptinclude with *.md pattern
+		includeFilePath := filepath.Join(tempDir, ".gptinclude")
+		if err := os.WriteFile(includeFilePath, []byte("*.md"), 0644); err != nil {
+			t.Fatalf("Failed to write .gptinclude file: %v", err)
+		}
+
+		// Create .gptignore with *.go pattern  
+		ignoreFilePath := filepath.Join(tempDir, ".gptignore")
+		if err := os.WriteFile(ignoreFilePath, []byte("*.go"), 0644); err != nil {
+			t.Fatalf("Failed to write .gptignore file: %v", err)
+		}
+
+		// Generate include and ignore lists
+		includeList := GenerateIncludeList(tempDir, "")
+		ignoreList := GenerateIgnoreList(tempDir, "", false)
+
+		// Process the repository
+		repo, err := ProcessGitRepo(tempDir, includeList, ignoreList)
+		if err != nil {
+			t.Fatalf("Failed to process repository: %v", err)
+		}
+
+		// Expected: Only .md files should be included (both root and nested)
+		expectedFiles := []string{"README.md", "docs/api.md"}
+		unexpectedFiles := []string{"file.go", "src/main.go", "deep/nested/file.go", "config.json", "src/config.json"}
+
+		// Check expected files are included
+		for _, expectedFile := range expectedFiles {
+			found := false
+			for _, file := range repo.Files {
+				if file.Path == expectedFile {
+					found = true
+					break
+				}
+			}
+			if !found {
+				t.Errorf("Expected file %s to be included, but it wasn't", expectedFile)
+			}
+		}
+
+		// Check unexpected files are excluded
+		for _, unexpectedFile := range unexpectedFiles {
+			for _, file := range repo.Files {
+				if file.Path == unexpectedFile {
+					t.Errorf("File %s should have been excluded, but it was included", unexpectedFile)
+					break
+				}
+			}
+		}
+	})
+
+	// Test case: Ensure existing patterns with ** still work
+	t.Run("Existing ** patterns should continue to work", func(t *testing.T) {
+		// Create .gptinclude with existing **/*.json pattern (should not be modified)
+		includeFilePath := filepath.Join(tempDir, ".gptinclude")
+		if err := os.WriteFile(includeFilePath, []byte("**/*.json"), 0644); err != nil {
+			t.Fatalf("Failed to write .gptinclude file: %v", err)
+		}
+
+		// Remove .gptignore for this test
+		ignoreFilePath := filepath.Join(tempDir, ".gptignore")
+		os.Remove(ignoreFilePath)
+
+		// Generate include and ignore lists
+		includeList := GenerateIncludeList(tempDir, "")
+		ignoreList := GenerateIgnoreList(tempDir, "", false)
+
+		// Process the repository
+		repo, err := ProcessGitRepo(tempDir, includeList, ignoreList)
+		if err != nil {
+			t.Fatalf("Failed to process repository: %v", err)
+		}
+
+		// Expected: Only nested .json files should be included (not root level)
+		expectedFiles := []string{"src/config.json"}
+		unexpectedFiles := []string{"config.json", "README.md", "file.go", "src/main.go"}
+
+		// Check expected files are included
+		for _, expectedFile := range expectedFiles {
+			found := false
+			for _, file := range repo.Files {
+				if file.Path == expectedFile {
+					found = true
+					break
+				}
+			}
+			if !found {
+				t.Errorf("Expected file %s to be included, but it wasn't", expectedFile)
+			}
+		}
+
+		// Check unexpected files are excluded  
+		for _, unexpectedFile := range unexpectedFiles {
+			for _, file := range repo.Files {
+				if file.Path == unexpectedFile {
+					t.Errorf("File %s should have been excluded, but it was included", unexpectedFile)
+					break
+				}
+			}
+		}
+	})
+}
\ No newline at end of file
diff --git a/prompt/prompt.go b/prompt/prompt.go
index 426ce30..7db51a8 100644
--- a/prompt/prompt.go
+++ b/prompt/prompt.go
@@ -53,7 +53,15 @@ func getIgnoreList(ignoreFilePath string) ([]string, error) {
 			line = line + "**"
 		}
 		line = strings.TrimPrefix(line, "/")
-		ignoreList = append(ignoreList, line)
+		
+		// Convert simple extension patterns like "*.ext" to match both root and nested files
+		// Add both "*.ext" (for root files) and "**/*.ext" (for nested files)
+		if strings.HasPrefix(line, "*.") && !strings.Contains(line, "/") && !strings.Contains(line, "**") {
+			ignoreList = append(ignoreList, line)        // Keep original for root files
+			ignoreList = append(ignoreList, "**/"+line)  // Add recursive pattern for nested files
+		} else {
+			ignoreList = append(ignoreList, line)
+		}
 	}
 	return ignoreList, scanner.Err()
 }
@@ -76,7 +84,15 @@ func getIncludeList(includeFilePath string) ([]string, error) {
 			line = line + "**"
 		}
 		line = strings.TrimPrefix(line, "/")
-		includeList = append(includeList, line)
+		
+		// Convert simple extension patterns like "*.ext" to match both root and nested files
+		// Add both "*.ext" (for root files) and "**/*.ext" (for nested files)
+		if strings.HasPrefix(line, "*.") && !strings.Contains(line, "/") && !strings.Contains(line, "**") {
+			includeList = append(includeList, line)        // Keep original for root files
+			includeList = append(includeList, "**/"+line)  // Add recursive pattern for nested files
+		} else {
+			includeList = append(includeList, line)
+		}
 	}
 	return includeList, scanner.Err()
 }