refactor: optimize fact extraction and module synthesis pipeline with…

.code-reducer.yaml

@@ -1,4 +1,4 @@
-model_id: gemma4:26b-a4b-it-qat
+model_id: ornith:9b
 ollama_base_url: http://localhost:11434
 ollama_num_ctx: 20000
 docs_dir: wiki
@@ -47,6 +47,9 @@ ignore:
   - go.mod
   - screenshots
   - examples
-  - docs
+  - gh-pages
   - LICENSE
   - AGENTS.md
+  - mkdocs.yml
+  - sonar-project.properties
+

cmd/cmd_test.go

@@ -97,27 +97,21 @@ func TestPromptStringList(t *testing.T) {
 	input := "a, b, c\n"
 	reader := bufio.NewReader(bytes.NewBufferString(input))
 
-	result, modified, err := promptStringList(reader, "Prompt", []string{"default"})
+	result, err := promptStringList(reader, "Prompt", []string{"default"})
 	if err != nil {
 		t.Errorf("Unexpected error: %v", err)
 	}
-	if !modified {
-		t.Errorf("Expected modified to be true")
-	}
 	if len(result) != 3 || result[0] != "a" || result[1] != "b" || result[2] != "c" {
 		t.Errorf("Unexpected result: %v", result)
 	}
 
 	// Test empty input falls back
 	input = "\n"
 	reader = bufio.NewReader(bytes.NewBufferString(input))
-	result, modified, err = promptStringList(reader, "Prompt", []string{"default"})
+	result, err = promptStringList(reader, "Prompt", []string{"default"})
 	if err != nil {
 		t.Errorf("Unexpected error: %v", err)
 	}
-	if modified {
-		t.Errorf("Expected modified to be false")
-	}
 	if len(result) != 1 || result[0] != "default" {
 		t.Errorf("Unexpected result: %v", result)
 	}
@@ -166,7 +160,7 @@ func TestPromptIgnores(t *testing.T) {
 func TestLoadInitialSetupConfig(t *testing.T) {
 	tmp := t.TempDir()
 	cfg := loadInitialSetupConfig(tmp)
-	if cfg.ModelID == "" || cfg.OllamaNumCtx <= 0 {
+	if cfg.ModelID == "" || cfg.OllamaNumCtx <= 0 || cfg.QuickstartPrompt == "" {
 		t.Fatalf("expected non-empty defaults, got %+v", cfg)
 	}
 
@@ -178,8 +172,8 @@ func TestLoadInitialSetupConfig(t *testing.T) {
 		t.Fatalf("failed to save config: %v", err)
 	}
 	loaded := loadInitialSetupConfig(tmp)
-	if loaded.ModelID != "custom-model" || loaded.OllamaNumCtx != 8192 {
-		t.Fatalf("expected custom values, got %+v", loaded)
+	if loaded.ModelID != "custom-model" || loaded.OllamaNumCtx != 8192 || loaded.QuickstartPrompt != config.DefaultQuickstartPrompt {
+		t.Fatalf("expected custom values and default prompts, got %+v", loaded)
 	}
 }
 
@@ -199,4 +193,7 @@ func TestRunSetupFlow(t *testing.T) {
 	if cfg.ModelID != config.OllamaDefaultModelID {
 		t.Errorf("expected default model ID, got %s", cfg.ModelID)
 	}
+	if cfg.QuickstartPrompt != config.DefaultQuickstartPrompt {
+		t.Errorf("expected default quickstart prompt, got %s", cfg.QuickstartPrompt)
+	}
 }

cmd/init.go

@@ -10,10 +10,7 @@ var initCmd = &cobra.Command{
 	Short: "Initialize project documentation",
 	Long:  `Scan the repository and build the initial set of wiki markdown pages.`,
 	RunE: func(cmd *cobra.Command, args []string) error {
-		if err := executeCommand(engine.ModeInit); err != nil {
-			return err
-		}
-		return nil
+		return executeCommand(engine.ModeInit)
 	},
 }
 

cmd/root.go

@@ -34,7 +34,7 @@ func init() {
 	RootCmd.PersistentFlags().StringVar(&numCtxFlag, "num-ctx", "", "Specify Ollama context window size")
 }
 
-func executeCommand(mode engine.Mode) error {
+func executeCommand(mode engine.RunMode) error {
 	repoRoot, err := os.Getwd()
 	if err != nil {
 		return fmt.Errorf("failed to get current working directory: %w", err)
@@ -61,53 +61,34 @@ func executeCommand(mode engine.Mode) error {
 }
 
 func checkAndRunSetup(repoRoot string) error {
-	needsSetup := !config.ConfigExists(repoRoot)
+	if config.ConfigExists(repoRoot) {
+		return nil
+	}
 	isTTY := isatty.IsTerminal(os.Stdin.Fd()) || isatty.IsCygwinTerminal(os.Stdin.Fd())
-
-	if needsSetup {
-		if !isTTY {
-			return fmt.Errorf("configuration file %s does not exist in the current directory. Please run 'code-reducer setup' to configure the application", config.ConfigFileName)
-		}
-
-		if err := RunSetupFlow(repoRoot); err != nil {
-			return err
-		}
+	if !isTTY {
+		return fmt.Errorf("configuration file %s does not exist in the current directory. Please run 'code-reducer setup' to configure the application", config.ConfigFileName)
 	}
-	return nil
+	return RunSetupFlow(repoRoot)
 }
 
-func checkInitStatus(repoRoot, docsDir string, mode engine.Mode) error {
+func checkInitStatus(repoRoot, docsDir string, mode engine.RunMode) error {
 	hasInit := engine.IsInitialized(repoRoot, docsDir)
 
-	if mode == engine.ModeInit {
-		if hasInit {
-			return fmt.Errorf("the project has already been initialized. Please use 'code-reducer update' to refresh documentation")
-		}
-	} else if mode == engine.ModeUpdate {
-		if !hasInit {
-			return fmt.Errorf("the project has not been initialized yet. Please run 'code-reducer init' first")
-		}
+	if mode == engine.ModeInit && hasInit {
+		return fmt.Errorf("the project has already been initialized. Please use 'code-reducer update' to refresh documentation")
+	}
+	if mode == engine.ModeUpdate && !hasInit {
+		return fmt.Errorf("the project has not been initialized yet. Please run 'code-reducer init' first")
 	}
 
 	return nil
 }
 
-func runEngine(repoRoot string, cfg *config.Config, mode engine.Mode) error {
+func runEngine(repoRoot string, cfg *config.Config, mode engine.RunMode) error {
 	ctx, stop := signal.NotifyContext(context.Background(), os.Interrupt, syscall.SIGTERM)
 	defer stop()
 
-	runner := engine.NewRunner(cfg)
-	err := runner.Run(ctx, repoRoot, mode, func(ev engine.Event) {
-		if ev.Type == engine.EventStatus {
-			fmt.Println(ev.Message)
-		} else if ev.Type == engine.EventError {
-			fmt.Fprintf(os.Stderr, "Error: %s\n", ev.Message)
-		} else {
-			fmt.Println(ev.Message)
-		}
-	})
-
-	if err != nil {
+	if err := engine.Run(ctx, repoRoot, cfg, mode, func(msg string) { fmt.Println(msg) }); err != nil {
 		return fmt.Errorf("documentation run failed: %w", err)
 	}
 

cmd/setup.go

@@ -32,47 +32,10 @@ func init() {
 
 func loadInitialSetupConfig(repoRoot string) *config.Config {
 	cfg, err := config.LoadConfig(repoRoot)
-	if err != nil || cfg == nil {
-		return &config.Config{
-			ModelID:                     config.OllamaDefaultModelID,
-			OllamaBaseURL:               config.OllamaDefaultBaseURL,
-			OllamaNumCtx:                config.OllamaDefaultNumCtx,
-			DocsDir:                     config.DefaultDocsDir,
-			ExtractionSteps:             config.DefaultExtractionSteps,
-			SystemPrompt:                config.DefaultSystemPrompt,
-			ModuleSynthesisPrompt:       config.DefaultModuleSynthesisPrompt,
-			ArchitecturePrompt:          config.DefaultArchitecturePrompt,
-			FileFactConsolidationPrompt: config.DefaultFileFactConsolidationPrompt,
-		}
-	}
-
-	if cfg.ModelID == "" {
-		cfg.ModelID = config.OllamaDefaultModelID
-	}
-	if cfg.OllamaBaseURL == "" {
-		cfg.OllamaBaseURL = config.OllamaDefaultBaseURL
-	}
-	if cfg.OllamaNumCtx <= 0 {
-		cfg.OllamaNumCtx = config.OllamaDefaultNumCtx
-	}
-	if cfg.DocsDir == "" {
-		cfg.DocsDir = config.DefaultDocsDir
-	}
-	if len(cfg.ExtractionSteps) == 0 {
-		cfg.ExtractionSteps = config.DefaultExtractionSteps
-	}
-	if cfg.SystemPrompt == "" {
-		cfg.SystemPrompt = config.DefaultSystemPrompt
-	}
-	if cfg.ModuleSynthesisPrompt == "" {
-		cfg.ModuleSynthesisPrompt = config.DefaultModuleSynthesisPrompt
-	}
-	if cfg.ArchitecturePrompt == "" {
-		cfg.ArchitecturePrompt = config.DefaultArchitecturePrompt
-	}
-	if cfg.FileFactConsolidationPrompt == "" {
-		cfg.FileFactConsolidationPrompt = config.DefaultFileFactConsolidationPrompt
+	if err != nil {
+		cfg = &config.Config{}
 	}
+	config.ApplyDefaults(cfg)
 	return cfg
 }
 
@@ -88,20 +51,11 @@ func promptContextSize(reader *bufio.Reader, defaultVal int) (int, error) {
 }
 
 func promptIgnores(reader *bufio.Reader, defaultIgnores []string) ([]string, error) {
-	userInputIgnores, ignoresModified, err := promptStringList(reader, "Enter directories, files, or patterns to ignore (comma-separated)", defaultIgnores)
+	ignores, err := promptStringList(reader, "Enter directories, files, or patterns to ignore (comma-separated)", defaultIgnores)
 	if err != nil {
 		return nil, fmt.Errorf("error reading ignores: %w", err)
 	}
-	if !ignoresModified {
-		if defaultIgnores != nil {
-			return defaultIgnores, nil
-		}
-		return []string{}, nil
-	}
-	if len(userInputIgnores) > 0 {
-		return userInputIgnores, nil
-	}
-	return []string{}, nil
+	return ignores, nil
 }
 
 // RunSetupFlow guides the user through setting up the configuration file.
@@ -139,64 +93,37 @@ func runSetupFlowWithReader(reader *bufio.Reader, repoRoot string) error {
 		return fmt.Errorf("error reading docs dir: %w", err)
 	}
 
-	newCfg := &config.Config{
-		ModelID:                     modelInput,
-		OllamaBaseURL:               urlInput,
-		OllamaNumCtx:                numCtx,
-		DocsDir:                     docsDirInput,
-		ExtractionSteps:             current.ExtractionSteps,
-		Ignore:                      ignores,
-		SystemPrompt:                current.SystemPrompt,
-		ModuleSynthesisPrompt:       current.ModuleSynthesisPrompt,
-		ArchitecturePrompt:          current.ArchitecturePrompt,
-		FileFactConsolidationPrompt: current.FileFactConsolidationPrompt,
-	}
+	current.ModelID = modelInput
+	current.OllamaBaseURL = urlInput
+	current.OllamaNumCtx = numCtx
+	current.DocsDir = docsDirInput
+	current.Ignore = ignores
 
-	err = config.SaveConfig(repoRoot, newCfg)
-	if err != nil {
+	if err := config.SaveConfig(repoRoot, current); err != nil {
 		return fmt.Errorf("error saving configuration: %w", err)
 	}
 	fmt.Printf("Configuration successfully saved to local %s file.\n", config.ConfigFileName)
 	return nil
 }
 
-func promptStringList(reader *bufio.Reader, promptMsg string, existingList []string) ([]string, bool, error) {
-	var result []string
-	existingStr := ""
-	if len(existingList) > 0 {
-		existingStr = strings.Join(existingList, ", ")
-	}
-
-	if existingStr == "" {
-		fmt.Printf("%s: ", promptMsg)
-	} else {
-		fmt.Printf("%s [%s]: ", promptMsg, existingStr)
-	}
-
-	input, err := reader.ReadString('\n')
+func promptStringList(reader *bufio.Reader, promptMsg string, existingList []string) ([]string, error) {
+	input, err := promptString(reader, promptMsg, strings.Join(existingList, ", "))
 	if err != nil {
-		return nil, false, err
-	}
-
-	input = strings.TrimSpace(input)
-	if input == "" {
-		return existingList, false, nil
+		return nil, err
 	}
 
 	lowerInput := strings.ToLower(input)
-	if lowerInput == "clear" || lowerInput == "none" {
-		return []string{}, true, nil
+	if input == "" || lowerInput == "clear" || lowerInput == "none" {
+		return []string{}, nil
 	}
 
-	parts := strings.Split(input, ",")
-	for _, part := range parts {
-		trimmed := strings.TrimSpace(part)
-		if trimmed != "" {
+	var result []string
+	for _, part := range strings.Split(input, ",") {
+		if trimmed := strings.TrimSpace(part); trimmed != "" {
 			result = append(result, trimmed)
 		}
 	}
-
-	return result, true, nil
+	return result, nil
 }
 
 func promptString(reader *bufio.Reader, promptMsg, existingVal string) (string, error) {

cmd/update.go

@@ -7,13 +7,10 @@ import (
 
 var updateCmd = &cobra.Command{
 	Use:   "update",
-	Short: "Update project documentation incrementally",
+	Short: "Incrementally update documentation for modified files using cached SHA-256 hashes.",
 	Long:  `Scan changed files since the last documented commit and update the wiki pages.`,
 	RunE: func(cmd *cobra.Command, args []string) error {
-		if err := executeCommand(engine.ModeUpdate); err != nil {
-			return err
-		}
-		return nil
+		return executeCommand(engine.ModeUpdate)
 	},
 }