Sync Install-Claude.sh with Install-Claude.ps1: Selective folder replacement

**Summary:**
Applied the same selective replacement logic from Install-Claude.ps1 to Install-Claude.sh (Bash version).

**Changes:**
- Added `backup_and_replace_directory` function for folder-level operations
- Modified `install_global` to use selective replacement for .claude, .codex, .gemini, .qwen
- Modified `install_path` to use selective replacement for local folders and config directories
- Maintained `merge_directory_contents` for backward compatibility

**New Installation Flow:**
1. Backup entire existing directory to timestamped backup folder
2. Only remove items in destination that match source item names
3. Copy source items to destination
4. Preserve all other files in destination directory

**Benefits:**
- Protects user-created files and session data
- Only updates files that come from installation source
- Safer incremental updates
- Consistent behavior across PowerShell and Bash versions

**Example:**
Source: .claude/{commands, workflows, scripts}
Destination before: .claude/{commands, workflows, custom.json, .workflow/}
Destination after: .claude/{commands, workflows, scripts, custom.json, .workflow/}

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>

Install-Claude.sh

@@ -340,6 +340,64 @@ function copy_file_to_destination() {
     fi
 }
 
+function backup_and_replace_directory() {
+    local source="$1"
+    local destination="$2"
+    local description="${3:-directory}"
+    local backup_folder="${4:-}"
+
+    if [ ! -d "$source" ]; then
+        write_color "WARNING: Source $description not found: $source" "$COLOR_WARNING"
+        return 1
+    fi
+
+    # Backup destination if it exists
+    if [ -d "$destination" ]; then
+        write_color "Found existing $description at: $destination" "$COLOR_INFO"
+
+        # Backup entire directory if backup is enabled
+        if [ "$NO_BACKUP" = false ] && [ -n "$backup_folder" ]; then
+            write_color "Backing up entire $description..." "$COLOR_INFO"
+            if backup_directory_to_folder "$destination" "$backup_folder"; then
+                write_color "Backed up $description to: $backup_folder" "$COLOR_SUCCESS"
+            fi
+        elif [ "$NO_BACKUP" = true ]; then
+            if ! confirm_action "Replace existing $description without backup?" false; then
+                write_color "Skipping $description installation" "$COLOR_WARNING"
+                return 1
+            fi
+        fi
+
+        # Get all items from source to determine what to clear in destination
+        write_color "Clearing conflicting items in destination $description..." "$COLOR_INFO"
+        while IFS= read -r -d '' source_item; do
+            local item_name=$(basename "$source_item")
+            local dest_item_path="${destination}/${item_name}"
+
+            if [ -e "$dest_item_path" ]; then
+                write_color "Removing existing: $item_name" "$COLOR_INFO"
+                rm -rf "$dest_item_path"
+            fi
+        done < <(find "$source" -mindepth 1 -maxdepth 1 -print0)
+        write_color "Cleared conflicting items in destination" "$COLOR_SUCCESS"
+    else
+        # Create destination directory if it doesn't exist
+        mkdir -p "$destination"
+        write_color "Created destination directory: $destination" "$COLOR_INFO"
+    fi
+
+    # Copy all items from source to destination
+    write_color "Copying $description from $source to $destination..." "$COLOR_INFO"
+    while IFS= read -r -d '' item; do
+        local item_name=$(basename "$item")
+        local dest_path="${destination}/${item_name}"
+        cp -r "$item" "$dest_path"
+    done < <(find "$source" -mindepth 1 -maxdepth 1 -print0)
+    write_color "$description installed successfully" "$COLOR_SUCCESS"
+
+    return 0
+}
+
 function merge_directory_contents() {
     local source="$1"
     local destination="$2"
@@ -447,25 +505,25 @@ function install_global() {
         fi
     fi
 
-    # Merge .claude directory contents
+    # Replace .claude directory (backup → clear conflicting → copy)
-    write_color "Merging .claude directory contents..." "$COLOR_INFO"
+    write_color "Installing .claude directory..." "$COLOR_INFO"
-    merge_directory_contents "$source_claude_dir" "$global_claude_dir" ".claude directory contents" "$backup_folder"
+    backup_and_replace_directory "$source_claude_dir" "$global_claude_dir" ".claude directory" "$backup_folder"
 
     # Handle CLAUDE.md file
     write_color "Installing CLAUDE.md to global .claude directory..." "$COLOR_INFO"
     copy_file_to_destination "$source_claude_md" "$global_claude_md" "CLAUDE.md" "$backup_folder"
 
-    # Merge .codex directory contents
+    # Replace .codex directory (backup → clear conflicting → copy)
-    write_color "Merging .codex directory contents..." "$COLOR_INFO"
+    write_color "Installing .codex directory..." "$COLOR_INFO"
-    merge_directory_contents "$source_codex_dir" "$global_codex_dir" ".codex directory contents" "$backup_folder"
+    backup_and_replace_directory "$source_codex_dir" "$global_codex_dir" ".codex directory" "$backup_folder"
 
-    # Merge .gemini directory contents
+    # Replace .gemini directory (backup → clear conflicting → copy)
-    write_color "Merging .gemini directory contents..." "$COLOR_INFO"
+    write_color "Installing .gemini directory..." "$COLOR_INFO"
-    merge_directory_contents "$source_gemini_dir" "$global_gemini_dir" ".gemini directory contents" "$backup_folder"
+    backup_and_replace_directory "$source_gemini_dir" "$global_gemini_dir" ".gemini directory" "$backup_folder"
 
-    # Merge .qwen directory contents
+    # Replace .qwen directory (backup → clear conflicting → copy)
-    write_color "Merging .qwen directory contents..." "$COLOR_INFO"
+    write_color "Installing .qwen directory..." "$COLOR_INFO"
-    merge_directory_contents "$source_qwen_dir" "$global_qwen_dir" ".qwen directory contents" "$backup_folder"
+    backup_and_replace_directory "$source_qwen_dir" "$global_qwen_dir" ".qwen directory" "$backup_folder"
 
     # Remove empty backup folder
     if [ -n "$backup_folder" ] && [ -d "$backup_folder" ]; then
@@ -528,11 +586,9 @@ function install_path() {
         local dest_folder="${local_claude_dir}/${folder}"
 
         if [ -d "$source_folder" ]; then
-            if [ -d "$dest_folder" ] && [ -n "$backup_folder" ]; then
+            # Use new backup and replace logic for local folders
-                backup_directory_to_folder "$dest_folder" "$backup_folder"
+            write_color "Installing local folder: $folder..." "$COLOR_INFO"
-            fi
+            backup_and_replace_directory "$source_folder" "$dest_folder" "$folder folder" "$backup_folder"
-
-            copy_directory_recursive "$source_folder" "$dest_folder"
             write_color "✓ Installed local folder: $folder" "$COLOR_SUCCESS"
         else
             write_color "WARNING: Source folder not found: $folder" "$COLOR_WARNING"
@@ -590,17 +646,17 @@ function install_path() {
     write_color "Installing CLAUDE.md to global .claude directory..." "$COLOR_INFO"
     copy_file_to_destination "$source_claude_md" "$global_claude_md" "CLAUDE.md" "$backup_folder"
 
-    # Merge .codex directory contents to local location
+    # Replace .codex directory to local location (backup → clear conflicting → copy)
-    write_color "Merging .codex directory contents to local location..." "$COLOR_INFO"
+    write_color "Installing .codex directory to local location..." "$COLOR_INFO"
-    merge_directory_contents "$source_codex_dir" "$local_codex_dir" ".codex directory contents" "$backup_folder"
+    backup_and_replace_directory "$source_codex_dir" "$local_codex_dir" ".codex directory" "$backup_folder"
 
-    # Merge .gemini directory contents to local location
+    # Replace .gemini directory to local location (backup → clear conflicting → copy)
-    write_color "Merging .gemini directory contents to local location..." "$COLOR_INFO"
+    write_color "Installing .gemini directory to local location..." "$COLOR_INFO"
-    merge_directory_contents "$source_gemini_dir" "$local_gemini_dir" ".gemini directory contents" "$backup_folder"
+    backup_and_replace_directory "$source_gemini_dir" "$local_gemini_dir" ".gemini directory" "$backup_folder"
 
-    # Merge .qwen directory contents to local location
+    # Replace .qwen directory to local location (backup → clear conflicting → copy)
-    write_color "Merging .qwen directory contents to local location..." "$COLOR_INFO"
+    write_color "Installing .qwen directory to local location..." "$COLOR_INFO"
-    merge_directory_contents "$source_qwen_dir" "$local_qwen_dir" ".qwen directory contents" "$backup_folder"
+    backup_and_replace_directory "$source_qwen_dir" "$local_qwen_dir" ".qwen directory" "$backup_folder"
 
     # Remove empty backup folder
     if [ -n "$backup_folder" ] && [ -d "$backup_folder" ]; then