Fix/issue #90 (#112)

* feat: add more templates

* refactor: update the help section for the scaffold command with new templates

* feat: add flags for recursive directory and hidden file / directory support

* feat: add symlink and directory support for the add command

* fix: progress bar breaking

* fix: ci warnings

Author: harshalranjhani

internal/chunk/chunkFile.go

@@ -69,6 +69,9 @@ func ChunkFile(ctx context.Context, filePath string, chunkSize int64, vaultRoot
 		return nil, fmt.Errorf("failed to initialize deduplication manager: %v", err)
 	}
 
+	// Set progress manager for coordinated output
+	dedupManager.SetProgressManager(progressMgr)
+
 	chunkRefs, err := processFileChunks(ctx, file, chunkSize, *vaultConfig, passphrase, dedupManager, progressMgr)
 	if err != nil {
 		return nil, err

internal/deduplication/manager.go

@@ -10,9 +10,15 @@ import (
 
 // Manager handles deduplication operations for a vault
 type Manager struct {
-	vaultRoot string
-	config    config.DeduplicationConfig
-	index     *DeduplicationIndex
+	vaultRoot   string
+	config      config.DeduplicationConfig
+	index       *DeduplicationIndex
+	progressMgr ProgressManager
+}
+
+// ProgressManager is an interface for progress reporting
+type ProgressManager interface {
+	PrintVerbose(format string, args ...interface{})
 }
 
 // NewManager creates a new deduplication manager
@@ -23,12 +29,18 @@ func NewManager(vaultRoot string, dedupConfig config.DeduplicationConfig) (*Mana
 	}
 
 	return &Manager{
-		vaultRoot: vaultRoot,
-		config:    dedupConfig,
-		index:     index,
+		vaultRoot:   vaultRoot,
+		config:      dedupConfig,
+		index:       index,
+		progressMgr: nil, // Will be set later if needed
 	}, nil
 }
 
+// SetProgressManager sets the progress manager for verbose output
+func (m *Manager) SetProgressManager(pm ProgressManager) {
+	m.progressMgr = pm
+}
+
 // ProcessChunk processes a chunk for deduplication
 // Returns: (chunkRef, deduplicated, error)
 func (m *Manager) ProcessChunk(chunkRef config.ChunkRef, chunkData []byte, storageHash string) (config.ChunkRef, bool, error) {
@@ -55,8 +67,10 @@ func (m *Manager) ProcessChunk(chunkRef config.ChunkRef, chunkData []byte, stora
 	if deduplicated {
 		// Chunk already exists, no need to store it again
 		chunkRef.Deduplicated = true
-		fmt.Printf("  └─ Deduplicated chunk %s (ref count: %d)\n",
-			chunkRef.Hash[:12], entry.RefCount)
+		if m.progressMgr != nil {
+			m.progressMgr.PrintVerbose("  └─ Deduplicated chunk %s (ref count: %d)\n",
+				chunkRef.Hash[:12], entry.RefCount)
+		}
 	} else {
 		// New chunk, store it
 		if err := m.storeChunk(storageHash, chunkData); err != nil {

internal/progress/progress.go

@@ -157,6 +157,11 @@ func (pm *Manager) FinishFileProgress() {
 // PrintVerbose prints verbose information if verbose mode is enabled
 func (pm *Manager) PrintVerbose(format string, args ...interface{}) {
 	if pm.options.Verbose {
+		// Clear the progress bar before printing to avoid line breaks
+		if pm.totalBar != nil {
+			_ = pm.totalBar.Clear() // #nosec G104 - progress bar clear is not critical for functionality
+		}
+
 		// #nosec G104 - verbose output errors are not critical for functionality
 		fmt.Printf(format, args...)
 		// Ensure output ends with newline if not already present
@@ -170,6 +175,11 @@ func (pm *Manager) PrintVerbose(format string, args ...interface{}) {
 // PrintInfo prints informational messages (unless quiet mode)
 func (pm *Manager) PrintInfo(format string, args ...interface{}) {
 	if !pm.options.Quiet {
+		// Clear the progress bar before printing to avoid line breaks
+		if pm.totalBar != nil {
+			_ = pm.totalBar.Clear() // #nosec G104 - progress bar clear is not critical for functionality
+		}
+
 		// #nosec G104 - info output errors are not critical for functionality
 		fmt.Printf(format, args...)
 	}